Immunogen platform

ABSTRACT

Aspects of the present invention relate to chimeric polypeptides including HCV NS3/4A sequences and T-cell epitopes. Embodiments include nucleic acids encoding the chimeric NS3/4A polypeptides, the encoded polypeptides, compositions containing said nucleic acids, compositions containing said chimeric polypeptides, as well as methods of making and using the aforementioned compositions including, but not limited to medicaments and vaccines.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of and claims the benefit of priorityto U.S. patent application Ser. No. 12/192,776, filed Aug. 15, 2008,which claims priority to U.S. Provisional Application No. 60/956,326,filed Aug. 16, 2007 and also claims priority to U.S. ProvisionalApplication No. 61/047,076, filed Apr. 22, 2008. All of theaforementioned applications are hereby expressly incorporated byreference in their entireties.

REFERENCE TO SEQUENCE LISTING

The present application is being filed along with a Sequence Listing inelectronic format. The Sequence Listing is provided as a file entitledSEQLIST-111C1.TXT, created Jul. 7, 2011, which is 4.7 MB in size. Theinformation in the electronic format of the Sequence Listing isincorporated herein by reference in its entirety.

BACKGROUND

Traditionally, vaccines have been based on live attenuated orinactivated pathogens. These strategies are inefficient, however,largely because of the antigenic variability of pathogens (e.g.,viruses). Several peptide vaccines that comprise antigenic peptides orpeptide fragments of pathogens have been developed. Conserved peptidefragments are less likely to exhibit antigenic variability and canovercome some of the problems associated with traditional peptides.Accordingly, subunit vaccines have been developed, which targetconserved regions of pathogens. Synthetic peptide vaccines tend to bepoorly immunogenic, however. The poor immunogenicity of syntheticpeptide vaccines may be attributed to the fact that although these typesof vaccines induce humoral antibody responses, they are less likely toinduce cell-mediated responses.

Several investigators have sought to improve the antigenicity ofsynthetic peptide vaccines. For example, Klein et al. describe theengineering of chimeric proteins that comprise an immunogenic region ofa protein from a first antigen linked to an immunogenic region from asecond pathogen. (See, U.S. Pat. Nos. 6,033,668; 6,017,539; 5,998,169;and 5,968,776). Others have sought to create chimeric proteins thatcouple B-cell epitopes to universal T-cell epitopes in order to improvethe immune response. (See, e.g., U.S. Pat. No. 5,114,713). Russell-Joneset al. (U.S. Pat. No. 5,928,644) also disclose T-cell epitopes derivedfrom the TraT protein of Escherichia coli, which are used to producehybrid molecules so as to generate an immune response to parasites,soluble factors (e.g., LSH) and viruses. Further, Ruslan (U.S. PatentApplication Publication No. 20030232055) discloses the manufacture ofvaccines based on PAMPs and immunogenic antigens. Despite theseadvances, the development of compositions and methods that improve theantigenicity of immunogens is manifest.

SUMMARY OF THE INVENTION

Several embodiments described herein concern compositions and methodsthat are useful for the generation, enhancement, or improvement of animmune response to a target antigen. Many platforms for the presentationof antigens are provided. These platforms are particularly useful fornucleic acid-based immunogens (e.g., DNA vaccines). It has beendiscovered that the hepatitis C virus (HCV) nonstructural protein 3(NS3) and nonstructural protein 4A (NS4A), collectively NS3/4A, andfragments of this fusion protein (e.g., fragments that retain theprotease domain, protease cleavage site, and/or the helicase domain) ora nucleic acid encoding these proteins are useful platforms to presentantigens (e.g., nucleic acids encoding a T cell epitope, such as a CTLor HTL domain) so as to generate a potent immune response to theassociated antigen.

One aim of using NS3/4A as a carrier or adjuvant is to effectivelyprovide T helper cells access to a fused antigen, thereby enhancing theimmune response to the fused antigen. In addition, in some embodimentsit is desired to have an active, or highly active, NS3/4A protease sincean enhanced or altered protease activity can have adjuvant effects thatimprove the immune response to the fused gene. Moreover, the activeNS3/4A protease can be used to cleave the fused protein (e.g., aheterologous antigen), especially when it contains inserted heterologousprotease cleavage sites, into smaller fragments to enhance processingand to ensure that the fused protein will not resemble its nativestructure. For certain conditions or diseases it can be desirable to usethe fused protein in a way that is structurally different from thenative form since the native form of the protein may have propertiesthat are at an immunogenic disadvantage. It is envisioned that theintroduction of foreign protease cleavage sites in the fusion protein(e.g., a peptide antigen) induce protein cleavage into small fragmentsthat can enhance processing. Additionally, if the natural sequence hasbeen changed the cleavage at the introduced sites can ensure that nonew, artificial junctional T cell epitopes are generated.

Accordingly, embodiments disclosed herein include compositions thatcomprise an isolated nucleic acid that encodes a chimeric Hepatitis Cvirus (HCV) NS3/4A polypeptide or a fragment thereof, which comprises asequence that encodes an antigen (preferably a non-HCV epitope or, whenan HCV epitope is used, the antigen is not in a position on the NS3/4Apeptide or NS3/4A nucleic acid or fragment thereof that is naturallyoccurring). The immunogenic sequence (e.g., a nucleic acid encoding anantigen) can be inserted within the NS3/4A nucleic acid or NS3/4Apeptide or attached thereto (e.g., the antigen-encoding nucleic acid canbe inserted within the nucleic acid encoding NS3 and/or NS4A domain at alocation outside of or within the protease domain, helicase domain, orprotease cleavage site or said sequence encoding said antigen can beflanking the 5′ or 3′ end of the nucleic acid encoding said HCV NS3/4Apeptide, such as juxtaposed to the 5′ or 3′ end).

Embodiments also include an antigenic or immunogenic peptide (e.g., apeptide of a pathogen, bacteria, toxin, virus, or cancer cell antigen)joined to (e.g., flanking or juxtaposed to) or affixed within NS3/4Apeptide or a fragment thereof, which peptide fragment can comprise atleast, equal to, greater than, less than, or any number in between 3, 5,10, 20, 50, 100, 150, 200, 250, 300, 350, 400, 500, 700, 1000, 1200, or1500 consecutive amino acids of a natural or synthetic NS3/4Apolypeptide (e.g., a naturally occurring isotype of NS3/4A or acodon-optimized or otherwise modified NS3/4A polypeptide (e.g.,consensus NS3/4A sequences generated from 2 or more istotypes), such asSEQ. ID. Nos. 2 and 36).

More embodiments include a nucleic acid that encodes an antigenic orimmunogenic peptide (e.g., a nucleic acid encoding a peptide of apathogen, bacteria, toxin, virus, or cancer cell antigen) joined to oraffixed within a nucleic acid encoding an NS3/4A peptide or a fragmentthereof (e.g., the nucleic acid that encodes said antigenic orimmunogenic peptide can be inserted within or joined to (e.g., flankingor juxtaposed to) an isolated but naturally occurring NS3/4A nucleicacid or a synthetic NS3/4A nucleic acid (e.g., a codon-optimized NS3/4Anucleic acid) or a fragment of these nucleic acids (e.g., the NS3/4anucleic acid fragment can comprise, consist of, or consist essentiallyof about at least, equal to, greater than, less than, or any number inbetween 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 400, 500,600, 700, 800, 900, 1000, 1200, 1500, 2000, or 2500 consecutivenucleotides of a nucleic acid sequence that encodes an isolated butnatural NS3/4A polypeptide or synthetic NS3/4A polypeptide (e.g., SEQ.ID. Nos. 1 and 35). Polypeptides encoded by said nucleic acids are alsoembodiments.

In some embodiments, the antigenic or immunogenic peptide is a T cellepitope (TCE), such as a CTL epitope or an HTL epitope, or the antigenicor immunogenic nucleic acid encodes a TCE, such as a CTL epitope or HTLepitope. As above, the TCE can be inserted within or flanking (e.g.,juxtaposed to) the NS3/4A peptide or nucleic acids encoding the NS3/4Apeptide or fragments of these peptides and nucleic acids, as describedabove, such that said chimeric sequences are or encode chimeric NS3/4Apolypeptides or fragments thereof with TCEs inserted within or flanking(e.g., juxtaposed to) the NS3/4A polypeptide sequences. Preferably, thenucleic acid encoding the TCE, and the encoded TCE, is located at aposition that is not naturally occurring in HCV, when said TCE is an HCVepitope. Desirably, the encoded NS3/4A chimeric polypeptide retainscatalytic activity (e.g., protease and/or helicase activity).

Accordingly, several embodiments include a nucleic acid that encodes aTCE (e.g., a CTL or HTL of a pathogen, bacteria, virus, toxin, or of acancer cell) inserted within or flanking (e.g., juxtaposed to) a nucleicacid encoding an NS3/4A polypeptide (e.g., SEQ. ID. Nos. 1 or 35) or anucleic acid encoding a fragment of an NS3/4A polypeptide (e.g., afragment of SEQ. ID. Nos. 1 or 35), preferably a fragment that retainsprotease and/or helicase activity, wherein said fragment can comprise,consist of, or consist essentially of about at least, equal to, greaterthan, less than, or any number in between 9, 15, 30, 50, 75, 100, 125,150, 175, 200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1200, 1500,2000, or 2500 consecutive nucleotides of a nucleic acid sequence thatencodes an isolated but natural NS3/4A polypeptide or synthetic NS3/4Apolypeptide (e.g., SEQ. ID. Nos. 1 or 35), such that when said TCE is asequence that encodes an HCV TCE, said HCV TCE is in a position on thenucleic acid or polypeptide encoded by said nucleic acid that is notnaturally occurring. Polypeptides encoding said nucleic acid embodimentsare also aspects of the invention.

Optionally, the isolated nucleic acids can also encode a linker sequenceand/or a sequence that promotes adjuvant activity (e.g., a stimulatoryTCE, a plurality of immune stimulatory di nucleotides, such as CpG, oran RNA binding domain). For example, in some embodiments, the linkersequence or adjuvant sequence flanks (e.g., juxtaposed to) at least oneend of the encoded TCE or antigen. Preferably, the nucleic acid encodesa linker comprising one to six alanine and/or glycine residues flankingor juxtaposed to at least one of a TCE, for example, between TCEsequences and N33/4A sequences. Polypeptides encoded by any of thenucleic acids provided herein are also embodiments.

In some embodiments, nucleic acids encoding an antigen, TCE, antigen andlinker, TCE and linker, antigen and adjuvant sequence, TCE and adjuvantsequence, antigen and linker and adjuvant sequence, or TCE and linkerand adjuvant sequence are inserted within a nucleic acid encoding an HCVNS3/4A polypeptide (e.g., SEQ ID NOs: 1 or 35) or fragment thereof(e.g., the NS3/4a nucleic acid fragment can comprise, consist of, orconsist essentially of about at least, equal to, greater than, lessthan, or any number in between 9, 15, 30, 50, 75, 100, 125, 150, 175,200, 250, 300, 400, 500, 600, 700, 800, 900, 1000, 1200, 1500, or 2000consecutive nucleotides of an NS3 and/or NS4A sequence, such as SEQ IDNOs: 1 or 35). Such embodiments can be used as DNA immunogens, which canbe delivered to a subject in need of an immune response to the antigencontained therein transdermally (e.g., a transdermal oil or patch), byinjection (e.g., hypodermic or ballistic), electroporation (e.g., genegun, microneedle, needless, ex vivo, MedPulsar™, electroporation withneedles or following needleless injection), or any combination thereof.Alternatively, polypeptides encoded by said DNA immunogens can bedelivered to a subject in need of an immune response to the antigen. Forexample, in some embodiments, a nucleic acid encoding an antigen, TCE,antigen and linker, TCE and linker, antigen and adjuvant sequence, TCEand adjuvant sequence, antigen and linker and adjuvant sequence, or TCEand linker and adjuvant sequence is inserted between the codons of anNS3/4A nucleic acid at sites that do not interrupt protease activityand/or helicase activity such that the expressed fusion peptide retainssuch catalytic activity and the nucleic acid immunogen is delivered to asubject in need of an immune response to said antigen or TCE by anelectroporation system that comprises a needle injection system (e.g.,Medpulser™). Again, aspects disclosed herein include polypeptides thatare encoded by said nucleic acids.

That is, in some embodiments, antigen, TCE, antigen and linker, TCE andlinker, antigen and adjuvant sequence, TCE and adjuvant sequence,antigen and linker and adjuvant sequence, or TCE and linker and adjuvantsequence are inserted between nucleotides 3 and 4, 6 and 7, 9 and 10, 12and 13, 15 and 16, 18 and 19, 21 and 22, 24 and 25, 27 and 28, 30 and31, 33 and 34, 36 and 37, 39 and 40, 42 and 43, 45 and 46, 48 and 49, 51and 52, 54 and 55, 57 and 58, 60 and 61, 63 and 64, 66 and 67, 69 and70, 72 and 73, 75 and 76, 78 and 79, 81 and 82, 84 and 85, 87 and 88, 90and 91, 93 and 94, 96 and 97, 99 and 100, 102 and 103, 105 and 106, 108and 109, 111 and 112, 114 and 115, 117 and 118, 120 and 121, 123 and124, 126 and 127, 129 and 130, 132 and 133, 125 and 136, 138 and 139,141 and 142, 144 and 145, 147 and 148, 150 and 151, 153 and 154, 156 and157, 159 and 160, 162 and 163, 165 and 166, 168 and 169, 171 and 172,174 and 175, 177 and 178, 180 and 181, 183 and 184, 186 and 187, 189 and19, 192 and 193, 195 and 196, 198 and 199, 201 and 202, 204 and 205, 207and 208, 210 and 211, 213 and 214, 216 and 217, 219 and 220, 222 and223, 225 and 226, 228 and 229, 231 and 232, 234 and 235, 237 and 238,240 and 241, 243 and 244, 246 and 247, 249 and 250, 252 and 253, 255 and256, 258 and 259, 261 and 262, 264 and 265, 267 and 268, 270 and 271,273 and 274, 276 and 277, 279 and 280, 282 and 283, 285 and 286, 288 and289, 291 and 292, 294 and 295, 297 and 298, 300 and 301, 303 and 304,306 and 307, 309 and 310, 312 and 313, 315 and 316, 318 and 319, 321 and322, 324 and 325, 327 and 328, 330 and 331, 333 and 334, 336 and 337,339 and 340, 342 and 343, 345 and 346, 348 and 349, 351 and 352, 354 and355, 357 and 358, 360 and 361, 363 and 364, 366 and 367, 369 and 370,372 and 373, 375 and 376, 378 and 379, 381 and 382, 24 and 385, 387 and388, 390 and 391, 393 and 394, 396 and 397, 399 and 400, 402 and 403,405 and 406, 408 and 409, 411 and 412, 414 and 415, 417 and 418, 420 and421, 423 and 424, 426 and 427, 429 and 430, 432 and 433, 435 and 436,438 and 439, 441 and 442, 444 and 445, 447 and 448, 450 and 451, 453 and454, 456 and 457, 459 and 460, 462 and 463, 465 and 466, 468 and 469,471 and 472, 474 and 475, 477 and 478, 480 and 481, 483 and 484, 486 and487, 489 and 490, 492 and 493, 495 and 496, 498 and 499, 501 and 502,504 and 505, 507 and 508, 510 and 511, 513 and 514, 516 and 517, 519 and520, 522 and 523, 525 and 526, 528 and 529, 531 and 532, 534 and 535,537 and 538, 540 and 541, 543 and 544, 546 and 547, 549 and 550, 552 and553, 555 and 556, 558 and 559, 561 and 562, 564 and 565, 567 and 568,570 and 571, 573 and 574, 576 and 577, 579 and 580, 582 and 583, 585 and586, 588 and 589, 591 and 592, 594 and 595, 597 and 598, 600 and 601,603 and 604, 606 and 607, 609 and 610, 612 and 613, 615 and 616, 618 and619, 621 and 622, 624 and 625, 627 and 628, 630 and 631, 633 and 634,636 and 637, 639 and 640, 642 and 643, 645 and 646, 648 and 649, 651 and652, 654 and 655, 657 and 658, 660 and 661, 663 and 664, 666 and 667,669 and 670, 672 and 673, 675 and 676, 678 and 679, 681 and 682, 684 and685, 687 and 688, 690 and 691, 693 and 694, 696 and 697, 699 and 700,702 and 703, 705 and 706, 708 and 709, 711 and 712, 714 and 715, 717 and718, 720 and 721, 723 and 724, 726 and 727, 729 and 730, 732 and 733,735 and 736, 738 and 739, 741 and 742, 744 and 745, 747 and 748, 750 and751, 753 and 754, 756 and 757, 759 and 760, 762 and 763, 765 and 766,768 and 769, 771 and 772, 774 and 775, 777 and 778, 780 and 781, 783 and784, 786 and 787, 789 and 790, 792 and 793, 795 and 796, 798 and 799,801 and 802, 804 and 805, 807 and 808, 810 and 811, 813 and 814, 816 and817, 819 and 820, 822 and 823, 825 and 826, 828 and 829, 831 and 832,834 and 835, 837 and 838, 840 and 841, 843 and 844, 846 and 847, 849 and850, 852 and 853, 855 and 856, 858 and 859, 861 and 862, 864 and 865,867 and 868, 870 and 871, 873 and 874, 876 and 877, 879 and 880, 882 and883, 885 and 886, 888 and 889, 891 and 892, 894 and 895, 897 and 898,900 and 901, 903 and 904, 906 and 907, 909 and 910, 912 and 913, 915 and916, 918 and 919, 921 and 922, 924 and 925, 927 and 928, 930 and 931,933 and 934, 936 and 937, 939 and 940, 942 and 943, 945 and 946, 948 and949, 951 and 952, 954 and 955, 957 and 958, 960 and 961, 963 and 964,966 and 967, 969 and 970, 972 and 973, 975 and 976, 978 and 979, 981 and982, 984 and 985, 987 and 988, 990 and 991, 993 and 994, 996 and 997,999 and 1000, 1002 and 1003, 1005 and 1006, 1008 and 1009, 1011 and1012, 1014 and 1015, 1017 and 1018, 1020 and 1021, 1023 and 1024, 1026and 1027, 1029 and 1030, 1032 and 1033, 1025 and 1036, 1038 and 1039,1041 and 1042, 1044 and 1045, 1047 and 1048, 1050 and 1051, 1053 and1054, 1056 and 1057, 1059 and 1060, 1062 and 1063, 1065 and 1066, 1068and 1069, 1071 and 1072, 1074 and 1075, 1077 and 1078, 1080 and 1081,1083 and 1084, 1086 and 1087, 1089 and 1090, 1092 and 1093, 1095 and1096, 1098 and 1099, 1101 and 1102, 1104 and 1105, 1107 and 1108, 1110and 1111, 1113 and 1114, 1116 and 1117, 1119 and 1120, 1122 and 1123,1125 and 1126, 1128 and 1129, 1131 and 1132, 1134 and 1135, 1137 and1138, 1140 and 1141, 1143 and 1144, 1146 and 1147, 1149 and 1150, 1152and 1153, 1155 and 1156, 1158 and 1159, 1161 and 1162, 1164 and 1165,1167 and 1168, 1170 and 1171, 1173 and 1174, 1176 and 1177, 1179 and1180, 1182 and 1183, 1185 and 1186, 1188 and 1189, 1191 and 1192, 1194and 1195, 1197 and 1198, 1200 and 1201, 1203 and 1204, 1206 and 1207,1209 and 1210, 1212 and 1213, 1215 and 1216, 1218 and 1219, 1221 and1222, 1224 and 1225, 1227 and 1228, 1230 and 1231, 1233 and 1234, 1236and 1237, 1239 and 1240, 1242 and 1243, 1245 and 1246, 1248 and 1249,1251 and 1252, 1254 and 1255, 1257 and 1258, 1260 and 1261, 1263 and1264, 1266 and 1267, 1269 and 1270, 1272 and 1273, 1275 and 1276, 1278and 1279, 1281 and 1282, 1284 and 1285, 1287 and 1288, 1290 and 1291,1293 and 1294, 1296 and 1297, 1299 and 1300, 1302 and 1303, 1305 and1306, 1308 and 1309, 1311 and 1312, 1314 and 1315, 1317 and 1318, 1320and 1321, 1323 and 1324, 1326 and 1327, 1329 and 1330, 1332 and 1333,1335 and 1336, 1338 and 1339, 1341 and 1342, 1344 and 1345, 1347 and1348, 1350 and 1351, 1353 and 1354, 1356 and 1357, 1359 and 1360, 1362and 1363, 1365 and 1366, 1368 and 1369, 1371 and 1372, 1374 and 1375,1377 and 1378, 1380 and 1381, 1383 and 1384, 1386 and 1387, 1389 and1390, 1392 and 1393, 1395 and 1396, 1398 and 1399, 1401 and 1402, 1404and 1405, 1407 and 1408, 1410 and 1411, 1413 and 1414, 1416 and 1417,1419 and 1420, 1422 and 1423, 1425 and 1426, 1428 and 1429, 1431 and1432, 1434 and 1435, 1437 and 1438, 1440 and 1441, 1443 and 1444, 1446and 1447, 1449 and 1450, 1452 and 1453, 1455 and 1456, 1458 and 1459,1461 and 1462, 1464 and 1465, 1467 and 1468, 1470 and 1471, 1473 and1474, 1476 and 1477, 1479 and 1480, 1482 and 1483, 1485 and 1486, 1488and 1489, 1491 and 1492, 1494 and 1495, 1497 and 1498, 1500 and 1501,1503 and 1504, 1506 and 1507, 1509 and 1510, 1512 and 1513, 1515 and1516, 1518 and 1519, 1521 and 1522, 1524 and 1525, 1527 and 1528, 1530and 1531, 1533 and 1534, 1536 and 1537, 1539 and 1540, 1542 and 1543,1545 and 1546, 1548 and 1549, 1551 and 1552, 1554 and 1555, 1557 and1558, 1560 and 1561, 1563 and 1564, 1566 and 1567, 1569 and 1570, 1572and 1573, 1575 and 1576, 1578 and 1579, 1581 and 1582, 1584 and 15685,1587 and 1588, 1590 and 1591, 1593 and 1594, 1596 and 1597, 1599 and1600, 1602 and 1603, 1605 and 1606, 1608 and 1609, 1611 and 1612, 1614and 1615, 1617 and 1618, 1620 and 1621, 1623 and 1624, 1626 and 1627,1629 and 1630, 1632 and 1633, 1635 and 1636, 1638 and 1639, 1641 and1642, 1644 and 1645, 1647 and 1648, 1650 and 1651, 1653 and 1654, 1656and 1657, 1659 and 1660, 1662 and 1663, 1665 and 1666, 1668 and 1669,1671 and 1672, 1674 and 1675, 1677 and 1678, 1680 and 1681, 1683 and1684, 1686 and 1687, 1689 and 1690, 1692 and 1693, 1695 and 1696, 1698and 1699, 1701 and 1702, 1704 and 1705, 1707 and 1708, 1710 and 1711,1713 and 1714, 1716 and 1717, 1719 and 1720, 1722 and 1723, 1725 and1726, 1728 and 1729, 1731 and 1732, 1734 and 1735, 1737 and 1738, 1740and 1741, 1743 and 1744, 1746 and 1747, 1749 and 1750, 1752 and 1753,1755 and 1756, 1758 and 1759, 1761 and 1762, 1764 and 1765, 1767 and1768, 1770 and 1771, 1773 and 1774, 1776 and 1777, 1779 and 1780, 1782and 1783, 1785 and 1786, 1788 and 1789, 1791 and 1792, 1794 and 1795,1797 and 1798, 1800 and 1801, 1803 and 1804, 1806 and 1807, 1809 and1810, 1812 and 1813, 1815 and 1816, 1818 and 1819, 1821 and 1822, 1824and 1825, 1827 and 1828, 1830 and 1831, 1833 and 1834, 1836 and 1837,1839 and 1840, 1842 and 1843, 1845 and 1846, 1848 and 1849, 1851 and1852, 1854 and 1855, 1857 and 1858, 1860 and 1861, 1863 and 1864, 1866and 1867, 1869 and 1870, 1872 and 1873, 1875 and 1876, 1878 and 1879,1881 and 1882, 1884 and 1885, 1887 and 1888, 1890 and 1891, 1893 and1894, 1896 and 1897, 1899 and 1900, 1902 and 1903, 1905 and 1906, 1908and 1909, 1911 and 1912, 1914 and 1915, 1917 and 1918, 1920 and 1921,1923 and 1924, 1926 and 1927, 1929 and 1930, 1932 and 1933, 1925 and1936, 1938 and 1939, 1941 and 1942, 1944 and 1945, 1947 and 1948, 1950and 1951, 1953 and 1954, 1956 and 157, 1959 and 1960, 1962 and 1963,1965 and 1966, 1968 and 1969, 1971 and 1972, 1974 and 175, 1977 and1978, 1980 and 1981, 1983 and 1984, 1986 and 1987, 1989 and 1999, 1992and 1993, 1995 and 1996, 1998 and 1999, 2001 and 2002, 2004 and 2005,2007 and 2008, 2010 and 2011, 2013 and 2014, 2016 and 2017, 2019 and2020, 2022 and 2023, 2025 and 2026, 2028 and 2029, 2031 and 2032, 2034and 2035, 2037 and 2038, 2040 and 2041, 2043 and 2044, 2046 and 2047,2049 and 2050, 2052 and 2053, 2055 and 2056, or 2058 and 2059 of anNS3/4A nucleic acid sequence such as SEQ ID NO: 1, an NS3/4A variant orconsensus nucleic acid sequence (e.g., an NS3/4A sequence developed froma plurality of NS3/4A isotypes, such as SEQ ID NO: 35), or any NS3/4Amutant (for example any nucleic acid encoding an NS3/4A with alteredprotease activity). Preferably, the nucleic acids encoding the insertedsequences retain the reading frame of the chimeric NS3/4A polypeptideand when the TCE encodes an HCV TCE, the sequence is inserted at aposition that is not naturally occurring. In some embodiments, the TCEis not an HCV peptide or peptide fragment. In preferred embodiments, thenucleic acid encoding the TCE can be inserted between nucleotides 1370and 1548 of SEQ ID NO:35, or in an analogous position in another NS3/4Acoding sequence. Aspects of the invention also include the polypeptidesencoded by the nucleic acid embodiments provided herein.

Accordingly, the nucleic acids encoding chimeric NS3/4A polypeptides canencode an antigen, TCE, antigen and linker, TCE and linker, antigen andadjuvant sequence, TCE and adjuvant sequence, antigen and linker andadjuvant sequence, or TCE and linker and adjuvant sequence insertedbetween amino acids 1 and 2, 2 and 3, 3 and 4, 4 and 5, 5 and 6, 6 and7, 7 and 8, 8 and 9, 9 and 10, 10 and 11, 11 and 12, 12 and 13, 13 and14, 14 and 15, 15 and 16, 16 and 17, 17 and 18, 18 and 19, 19 and 20, 20and 21, 21 and 22, 22 and 23, 23 and 24, 24 and 25, 25 and 26, 26 and27, 27 and 28, 28 and 29, 29 and 30, 30 and 31, 31 and 32, 32 and 33, 33and 34, 34 and 35, 35 and 36, 36 and 37, 37 and 38, 38 and 39, 39 and40, 40 and 41, 41 and 42, 42 and 43, 43 and 44, 44 and 45, 45 and 46, 46and 47, 47 and 48, 48 and 49, 49 and 50, 50 and 51, 51 and 52, 52 and53, 53 and 54, 54 and 55, 55 and 56, 56 and 57, 57 and 58, 58 and 59, 59and 60, 60 and 61, 61 and 62, 62 and 63, 63 and 64, 64 and 65, 65 and66, 66 and 67, 67 and 68, 68 and 69, 69 and 70, 70 and 71, 71 and 72, 72and 73, 73 and 74, 74 and 75, 75 and 76, 76 and 77, 77 and 78, 78 and79, 79 and 80, 80 and 81, 81 and 82, 82 and 83, 83 and 84, 84 and 85, 85and 86, 86 and 87, 87 and 88, 88 and 89, 89 and 90, 90 and 91, 91 and92, 92 and 93, 93 and 94, 94 and 95, 95 and 96, 96 and 97, 97 and 98, 98and 99, 99 and 100, 100 and 101, 101 and 102, 102 and 103, 103 and 104,104 and 105, 105 and 106, 106 and 107, 107 and 108, 108 and 109, 109 and110, 110 and 111, 111 and 112, 112 and 113, 113 and 114, 114 and 115,115 and 116, 116 and 117, 117 and 118, 118 and 119, 119 and 120, 120 and121, 121 and 122, 122 and 123, 123 and 124, 124 and 125, 125 and 126,126 and 127, 127 and 128, 128 and 129, 129 and 130, 130 and 131, 131 and132, 132 and 133, 133 and 134, 134 and 135, 135 and 136, 136 and 137,137 and 138, 138 and 139, 139 and 140, 140 and 141, 141 and 142, 142 and143, 143 and 144, 144 and 145, 145 and 146, 146 and 147, 147 and 148,148 and 149, 149 and 150, 150 and 151, 151 and 152, 152 and 153, 153 and154, 154 and 155, 155 and 156, 156 and 157, 157 and 158, 158 and 159,159 and 160, 160 and 161, 161 and 162, 162 and 163, 163 and 164, 164 and165, 165 and 166, 166 and 167, 167 and 168, 168 and 169, 169 and 170,170 and 171, 171 and 172, 172 and 173, 173 and 174, 174 and 175, 175 and176, 176 and 177, 177 and 178, 178 and 179, 179 and 180, 180 and 181,181 and 182, 182 and 183, 183 and 184, 184 and 185, 185 and 186, 186 and187, 187 and 188, 188 and 189, 189 and 190, 190 and 191, 191 and 192,192 and 193, 193 and 194, 194 and 195, 195 and 196, 196 and 197, 197 and198, 198 and 199, 199 and 200, 200 and 201, 201 and 202, 202 and 203,203 and 204, 204 and 205, 205 and 206, 206 and 207, 207 and 208, 208 and209, 209 and 210, 210 and 211, 211 and 212, 212 and 213, 213 and 214,214 and 215, 215 and 216, 216 and 217, 217 and 218, 218 and 219, 219 and220, 220 and 221, 221 and 222, 222 and 223, 223 and 224, 224 and 225,225, and 226, 226 and 227, 227 and 228, 228 and 229, 229 and 230, 230and 231, 231 and 232, 232 and 233, 233 and 234, 234 and 235, 235 and236, 236 and 237, 237 and 238, 238 and 239, 239 and 240, 240 and 241,241 and 242, 242 and 243, 243 and 244, 244 and 245, 245 and 246, 246 and247, 247 and 248, 248 and 249, 249 and 250, 250 and 251, 251 and 252,252 and 253, 253 and 254, 254 and 255, 255 and 256, 256 and 257, 257 and258, 258 and 259, 259 and 260, 260 and 261, 261 and 262, 262 and 263,263 and 264, 264 and 265, 265 and 266, 266 and 267, 267 and 268, 268 and269, 269 and 270, 270 and 271, 271 and 272, 272 and 273, 273 and 274,274 and 275, 275 and 276, 276 and 277, 277 and 278, 278 and 279, 279 and280, 280 and 281, 281 and 282, 282 and 283, 283 and 284, 284 and 285,285 and 286, 286 and 287, 287 and 288, 288 and 289, 289 and 290, 290 and291, 291 and 292, 292 and 293, 293 and 294, 294 and 295, 295 and 296,296 and 297, 297 and 298, 298 and 299, 299 and 300, 300 and 201, 301 and302, 302 and 303, 303 and 304, 304 and 305, 305 and 306, 306 and 307,307 and 308, 308 and 309, 309 and 310, 310 and 311, 311 and 312, 312 and313, 313 and 314, 314 and 315, 315 and 316, 316 and 317, 317 and 318,318 and 319, 319 and 320, 320 and 321, 321, and 322, 322 and 323, 323and 324, 324 and 325, 325, and 326, 326 and 327, 327 and 328, 328 and329, 329 and 330, 330 and 331, 331 and 332, 332 and 333, 333 and 334,334 and 335, 335 and 336, 336 and 337, 337 and 338, 338 and 339, 339 and340, 340 and 341, 341 and 342, 342 and 343, 343 and 344, 344 and 345,345 and 346, 346 and 347, 347 and 348, 348 and 349, 349 and 350, 350 and351, 351 and 352, 352 and 353, 353 and 354, 354 and 355, 355 and 356,356 and 357, 357 and 358, 358 and 359, 359 and 360, 360 and 361, 361 and362, 362 and 363, 363 and 364, 364 and 365, 365 and 366, 366 and 367,367 and 368, 368 and 369, 369 and 370, 370 and 371, 371 and 372, 372 and373, 373 and 374, 374 and 375, 375 and 376, 376 and 377, 377 and 378,378 and 379, 379 and 380, 380 and 381, 381 and 382, 382 and 383, 383 and384, 384 and 385, 385 and 386, 386 and 387, 387 and 388, 388 and 389,389 and 390, 390 and 391, 391 and 392, 392 and 393, 393 and 394, 394 and395, 395 and 396, 396 and 397, 397 and 398, 398 and 399, 399 and 400,401 and 402, 402 and 403, 403 and 404, 404 and 405, 405 and 406, 406 and407, 407 and 408, 408 and 409, 409 and 410, 410 and 411, 411 and 412,412 and 413, 413 and 414, 414 and 415, 415 and 416, 416 and 417, 417 and418, 418 and 419, 419 and 420, 420 and 421, 421 and 422, 422 and 423,423 and 424, 424 and 425, 425 and 426, 426 and 427, 427 and 428, 428 and429, 429 and 430, 430 and 431, 431 and 432, 432 and 433, 433 and 434,434 and 435, 435 and 436, 436 and 437, 437 and 438, 438 and 439, 439 and440, 440 and 441, 441 and 442, 442 and 443, 443 and 444, 444 and 445,445 and 446, 446 and 447, 447 and 448, 448 and 449, 449 and 450, 450 and451, 451 and 452, 452 and 453, 453 and 454, 454 and 455, 455 and 456,456 and 457, 457 and 458, 458 and 459, 459 and 460, 460 and 461, 461 and462, 462 and 463, 463 and 464, 464 and 465, 465 and 466, 466 and 467,467 and 468, 468 and 469, 469 and 470, 470 and 471, 471 and 472, 472 and473, 473 and 474, 474 and 475, 475 and 476, 476 and 477, 477 and 478,478 and 479, 479 and 480, 480 and 481, 481 and 482, 482 and 483, 483 and484, 484 and 485, 485 and 486, 486 and 487, 487 and 488, 488 and 489,489 and 490, 490 and 491, 491 and 492, 492 and 493, 493 and 494, 494 and495, 495 and 496, 496 and 497, 497 and 498, 498 and 499, 499 and 500,501 and 502, 502 and 503, 503 and 504, 504 and 505, 505 and 506, 506 and507, 507 and 508, 508 and 509, 509 and 510, 510 and 511, 511 and 512,512 and 513, 513 and 514, 514 and 515, 515 and 516, 516 and 517, 517 and518, 518 and 519, 519 and 520, 520 and 521, 521 and 522, 522 and 523,523 and 524, 524 and 525, 525 and 526, 526 and 527, 527 and 528, 528 and529, 529 and 530, 530 and 531, 531 and 532, 532 and 533, 533 and 534,534 and 535, 535 and 536, 536 and 537, 537 and 538, 538 and 539, 539 and540, 540 and 541, 541 and 542, 542 and 543, 543 and 544, 544 and 545,545 and 546, 546 and 547, 547 and 548, 548 and 549, 549 and 550, 550 and551, 551 and 552, 552 and 553, 553 and 554, 554 and 555, 555 and 556,556 and 557, 557 and 558, 558 and 559, 559 and 560, 560 and 561, 561 and562, 562 and 563, 563 and 564, 564 and 565, 565 and 566, 566 and 567,567 and 568, 568 and 569, 569 and 570, 570 and 571, 571 and 572, 572 and573, 573 and 574, 574 and 575, 575 and 576, 576 and 577, 577 and 578,578 and 579, 579 and 580, 580 and 581, 581 and 582, 582 and 583, 583 and584, 584 and 585, 585 and 586, 586 and 587, 587 and 588, 588 and 589,589 and 590, 590 and 591, 591 and 592, 592 and 593, 593 and 594, 594 and595, 595 and 596, 596 and 597, 597 and 598, 598 and 599, 599 and 600,601 and 602, 602 and 603, 603 and 604, 604 and 605, 605 and 606, 606 and607, 607 and 608, 608 and 609, 609 and 610, 610 and 611, 611 and 612,612 and 613, 613 and 614, 614 and 615, 615 and 616, 616 and 617, 617 and618, 618 and 619, 619 and 620, 620 and 621, 621 and 622, 622 and 623,623 and 624, 624 and 625, 625 and 626, 626 and 627, 627 and 628, 628 and629, 629 and 630, 630 and 631, 631 and 632, 632 and 633, 633 and 634,634 and 635, 635 and 636, 636 and 637, 637 and 638, 638 and 639, 639 and640, 640 and 641, 641 and 642, 642 and 643, 643 and 644, 644 and 645,645 and 646, 646 and 647, 647 and 648, 648 and 649, 649 and 650, 650 and651, 651 and 652, 652 and 653, 653 and 654, 654 and 655, 655 and 656,656 and 657, 657 and 658, 658 and 659, 659 and 660, 660 and 661, 661 and662, 662 and 663, 663 and 664, 664 and 665, 665 and 666, 666 and 667,667 and 668, 668 and 669, 669 and 670, 670 and 671, 671 and 672, 72 and673, 673 and 674, 674 and 675, 675 and 676, 676 and 677, 677 and 678,678 and 679, 679 and 680, 680 and 681, 681 and 682, 682 and 683, 683 and684, 684 and 685, or 685 and 686 of an NS3/4A polypeptide (e.g., SEQ IDNO: 2) an NS3/4A variant polypeptide (e.g., SEQ ID NO: 36), or anyNS3/4A mutant (for example any NS3/4A with altered protease activity).In preferred embodiments, the antigen, TCE, antigen and linker, TCE andlinker, antigen and adjuvant sequence, TCE and adjuvant sequence,antigen and linker and adjuvant sequence, or TCE and linker and adjuvantsequence inserted between amino acids 453 and 513 of SEQ ID NO:36 or ananalogous position in an NS3/4A polypeptide. The encoded polypeptides ofthe nucleic acid embodiments described herein are also embodiments.

In some embodiments, the encoded antigen, TCE, antigen and linker, TCEand linker, antigen and adjuvant sequence, TCE and adjuvant sequence,antigen and linker and adjuvant sequence, or TCE and linker and adjuvantsequence is juxtaposed to or flanking the HCV NS3/4A polypeptide orfragment thereof. For example, the nucleic acid encoding the antigen,TCE, antigen and linker, TCE and linker, antigen and adjuvant sequence,TCE and adjuvant sequence, antigen and linker and adjuvant sequence, orTCE and linker and adjuvant sequence can be 5′ to the nucleic acidencoding the HCV NS3/4A polypeptide or fragment thereof, such that theTCE is on the N-terminal end of the encoded chimeric polypeptide.Optionally, the nucleic acid encoding the antigen, TCE, antigen andlinker, TCE and linker, antigen and adjuvant sequence, TCE and adjuvantsequence, antigen and linker and adjuvant sequence, or TCE and linkerand adjuvant sequence can be 3′ to the nucleic acid encoding the HCVNS3/4A polypeptide or fragment thereof, such that the TCE is on theC-terminal end of the encoded chimeric polypeptide.

The antigens and/or TCE used in the platforms described herein caninclude, but are not limited to, nucleic acids that encode viralantigens, bacterial antigens, parasitic antigens, tumor antigens, andtoxins. In some embodiments, the encoded TCE comprises a sequenceselected from the group consisting of SEQ ID NOs: 221-571 and SEQ IDNOs: 809-1011 and SEQ ID NO:1014 and SEQ ID NOs: 1016-1034 and SEQ IDNOs: 1146-1173 and SEQ ID NOs: 1210-1328. In preferred embodiments, theencoded TCE or antigen is obtained from a hepatitis virus, such as anantigen from the Hepatitis A virus (HAV), Hepatitis B virus (HBV), orHCV, HIV, a flu virus, an allergen (such as Birch allergen), or malaria.For example, in some embodiments, the encoded TCE comprises the aminoacid sequence of SEQ ID NO:1014. Antigens and TCEs that are present onpathogens that infect domestic animals are also embodied. That is, someembodiments include veterinary preparations that comprise a nucleic acidencoding an NS3/4A platform, as described herein, and an antigen presenton an animal pathogen (e.g., swine flu, avian flu, or equine flu).

Some embodiments also concern the chimeric polypeptides encoded by thenucleic acids disclosed herein. In some embodiments, the chimericpolypeptide encoded by the isolated nucleic acid retains NS3A proteaseactivity and/or NS3A helicase activity and/or a protease cleavage site.Optionally, the chimeric polypeptides include a linker or adjuvantpolypeptide (e.g., an RNA binding domain, such as poly Arg). Forexample, in some embodiments, the linker flanks at least one end (i.e.,N-terminal or C-terminal end) of the TCE. In some embodiments, a linkercomprising one to six alanine and/or glycine residues is flanking orjuxtaposed to at least one end of the TCE, such as between NS3/4A aminoacid sequences and TCE sequences.

Also provided herein are NS3/4A chimeric polypeptides that includeNS3/4A polypeptides or variants, or fragments thereof and at least oneantigen, TCE, antigen and linker, TCE and linker, antigen and adjuvantsequence, TCE and adjuvant sequence, antigen and linker and adjuvantsequence, or TCE and linker and adjuvant sequence. Optionally, thesesequences are inserted within the HCV NS3/4A polypeptide or fragmentthereof. For example, the chimeric NS3/4A polypeptides can consist of,consist essentially of, or comprise an antigen, TCE, antigen and linker,TCE and linker, antigen and adjuvant sequence, TCE and adjuvantsequence, antigen and linker and adjuvant sequence, or TCE and linkerand adjuvant sequence inserted between amino acids 1 and 2, 2 and 3, 3and 4, 4 and 5, 5 and 6, 6 and 7, 7 and 8, 8 and 9, 9 and 10, 10 and 11,11 and 12, 12 and 13, 13 and 14, 14 and 15, 15 and 16, 16 and 17, 17 and18, 18 and 19, 19 and 20, 20 and 21, 21 and 22, 22 and 23, 23 and 24, 24and 25, 25 and 26, 26 and 27, 27 and 28, 28 and 29, 29 and 30, 30 and31, 31 and 32, 32 and 33, 33 and 34, 34 and 35, 35 and 36, 36 and 37, 37and 38, 38 and 39, 39 and 40, 40 and 41, 41 and 42, 42 and 43, 43 and44, 44 and 45, 45 and 46, 46 and 47, 47 and 48, 48 and 49, 49 and 50, 50and 51, 51 and 52, 52 and 53, 53 and 54, 54 and 55, 55 and 56, 56 and57, 57 and 58, 58 and 59, 59 and 60, 60 and 61, 61 and 62, 62 and 63, 63and 64, 64 and 65, 65 and 66, 66 and 67, 67 and 68, 68 and 69, 69 and70, 70 and 71, 71 and 72, 72 and 73, 73 and 74, 74 and 75, 75 and 76, 76and 77, 77 and 78, 78 and 79, 79 and 80, 80 and 81, 81 and 82, 82 and83, 83 and 84, 84 and 85, 85 and 86, 86 and 87, 87 and 88, 88 and 89, 89and 90, 90 and 91, 91 and 92, 92 and 93, 93 and 94, 94 and 95, 95 and96, 96 and 97, 97 and 98, 98 and 99, 99 and 100, 100 and 101, 101 and102, 102 and 103, 103 and 104, 104 and 105, 105 and 106, 106 and 107,107 and 108, 108 and 109, 109 and 110, 110 and 111, 111 and 112, 112 and113, 113 and 114, 114 and 115, 115 and 116, 116 and 117, 117 and 118,118 and 119, 119 and 120, 120 and 121, 121 and 122, 122 and 123, 123 and124, 124 and 125, 125 and 126, 126 and 127, 127 and 128, 128 and 129,129 and 130, 130 and 131, 131 and 132, 132 and 133, 133 and 134, 134 and135, 135 and 136, 136 and 137, 137 and 138, 138 and 139, 139 and 140,140 and 141, 141 and 142, 142 and 143, 143 and 144, 144 and 145, 145 and146, 146 and 147, 147 and 148, 148 and 149, 149 and 150, 150 and 151,151 and 152, 152 and 153, 153 and 154, 154 and 155, 155 and 156, 156 and157, 157 and 158, 158 and 159, 159 and 160, 160 and 161, 161 and 162,162 and 163, 163 and 164, 164 and 165, 165 and 166, 166 and 167, 167 and168, 168 and 169, 169 and 170, 170 and 171, 171 and 172, 172 and 173,173 and 174, 174 and 175, 175 and 176, 176 and 177, 177 and 178, 178 and179, 179 and 180, 180 and 181, 181 and 182, 182 and 183, 183 and 184,184 and 185, 185 and 186, 186 and 187, 187 and 188, 188 and 189, 189 and190, 190 and 191, 191 and 192, 192 and 193, 193 and 194, 194 and 195,195 and 196, 196 and 197, 197 and 198, 198 and 199, 199 and 200, 200 and201, 201 and 202, 202 and 203, 203 and 204, 204 and 205, 205 and 206,206 and 207, 207 and 208, 208 and 209, 209 and 210, 210 and 211, 211 and212, 212 and 213, 213 and 214, 214 and 215, 215 and 216, 216 and 217,217 and 218, 218 and 219, 219 and 220, 220 and 221, 221 and 222, 222 and223, 223 and 224, 224 and 225, 225, and 226, 226 and 227, 227 and 228,228 and 229, 229 and 230, 230 and 231, 231 and 232, 232 and 233, 233 and234, 234 and 235, 235 and 236, 236 and 237, 237 and 238, 238 and 239,239 and 240, 240 and 241, 241 and 242, 242 and 243, 243 and 244, 244 and245, 245 and 246, 246 and 247, 247 and 248, 248 and 249, 249 and 250,250 and 251, 251 and 252, 252 and 253, 253 and 254, 254 and 255, 255 and256, 256 and 257, 257 and 258, 258 and 259, 259 and 260, 260 and 261,261 and 262, 262 and 263, 263 and 264, 264 and 265, 265 and 266, 266 and267, 267 and 268, 268 and 269, 269 and 270, 270 and 271, 271 and 272,272 and 273, 273 and 274, 274 and 275, 275 and 276, 276 and 277, 277 and278, 278 and 279, 279 and 280, 280 and 281, 281 and 282, 282 and 283,283 and 284, 284 and 285, 285 and 286, 286 and 287, 287 and 288, 288 and289, 289 and 290, 290 and 291, 291 and 292, 292 and 293, 293 and 294,294 and 295, 295 and 296, 296 and 297, 297 and 298, 298 and 299, 299 and300, 300 and 201, 301 and 302, 302 and 303, 303 and 304, 304 and 305,305 and 306, 306 and 307, 307 and 308, 308 and 309, 309 and 310, 310 and311, 311 and 312, 312 and 313, 313 and 314, 314 and 315, 315 and 316,316 and 317, 317 and 318, 318 and 319, 319 and 320, 320 and 321, 321,and 322, 322 and 323, 323 and 324, 324 and 325, 325, and 326, 326 and327, 327 and 328, 328 and 329, 329 and 330, 330 and 331, 331 and 332,332 and 333, 333 and 334, 334 and 335, 335 and 336, 336 and 337, 337 and338, 338 and 339, 339 and 340, 340 and 341, 341 and 342, 342 and 343,343 and 344, 344 and 345, 345 and 346, 346 and 347, 347 and 348, 348 and349, 349 and 350, 350 and 351, 351 and 352, 352 and 353, 353 and 354,354 and 355, 355 and 356, 356 and 357, 357 and 358, 358 and 359, 359 and360, 360 and 361, 361 and 362, 362 and 363, 363 and 364, 364 and 365,365 and 366, 366 and 367, 367 and 368, 368 and 369, 369 and 370, 370 and371, 371 and 372, 372 and 373, 373 and 374, 374 and 375, 375 and 376,376 and 377, 377 and 378, 378 and 379, 379 and 380, 380 and 381, 381 and382, 382 and 383, 383 and 384, 384 and 385, 385 and 386, 386 and 387,387 and 388, 388 and 389, 389 and 390, 390 and 391, 391 and 392, 392 and393, 393 and 394, 394 and 395, 395 and 396, 396 and 397, 397 and 398,398 and 399, 399 and 400, 401 and 402, 402 and 403, 403 and 404, 404 and405, 405 and 406, 406 and 407, 407 and 408, 408 and 409, 409 and 410,410 and 411, 411 and 412, 412 and 413, 413 and 414, 414 and 415, 415 and416, 416 and 417, 417 and 418, 418 and 419, 419 and 420, 420 and 421,421 and 422, 422 and 423, 423 and 424, 424 and 425, 425 and 426, 426 and427, 427 and 428, 428 and 429, 429 and 430, 430 and 431, 431 and 432,432 and 433, 433 and 434, 434 and 435, 435 and 436, 436 and 437, 437 and438, 438 and 439, 439 and 440, 440 and 441, 441 and 442, 442 and 443,443 and 444, 444 and 445, 445 and 446, 446 and 447, 447 and 448, 448 and449, 449 and 450, 450 and 451, 451 and 452, 452 and 453, 453 and 454,454 and 455, 455 and 456, 456 and 457, 457 and 458, 458 and 459, 459 and460, 460 and 461, 461 and 462, 462 and 463, 463 and 464, 464 and 465,465 and 466, 466 and 467, 467 and 468, 468 and 469, 469 and 470, 470 and471, 471 and 472, 472 and 473, 473 and 474, 474 and 475, 475 and 476,476 and 477, 477 and 478, 478 and 479, 479 and 480, 480 and 481, 481 and482, 482 and 483, 483 and 484, 484 and 485, 485 and 486, 486 and 487,487 and 488, 488 and 489, 489 and 490, 490 and 491, 491 and 492, 492 and493, 493 and 494, 494 and 495, 495 and 496, 496 and 497, 497 and 498,498 and 499, 499 and 500, 501 and 502, 502 and 503, 503 and 504, 504 and505, 505 and 506, 506 and 507, 507 and 508, 508 and 509, 509 and 510,510 and 511, 511 and 512, 512 and 513, 513 and 514, 514 and 515, 515 and516, 516 and 517, 517 and 518, 518 and 519, 519 and 520, 520 and 521,521 and 522, 522 and 523, 523 and 524, 524 and 525, 525 and 526, 526 and527, 527 and 528, 528 and 529, 529 and 530, 530 and 531, 531 and 532,532 and 533, 533 and 534, 534 and 535, 535 and 536, 536 and 537, 537 and538, 538 and 539, 539 and 540, 540 and 541, 541 and 542, 542 and 543,543 and 544, 544 and 545, 545 and 546, 546 and 547, 547 and 548, 548 and549, 549 and 550, 550 and 551, 551 and 552, 552 and 553, 553 and 554,554 and 555, 555 and 556, 556 and 557, 557 and 558, 558 and 559, 559 and560, 560 and 561, 561 and 562, 562 and 563, 563 and 564, 564 and 565,565 and 566, 566 and 567, 567 and 568, 568 and 569, 569 and 570, 570 and571, 571 and 572, 572 and 573, 573 and 574, 574 and 575, 575 and 576,576 and 577, 577 and 578, 578 and 579, 579 and 580, 580 and 581, 581 and582, 582 and 583, 583 and 584, 584 and 585, 585 and 586, 586 and 587,587 and 588, 588 and 589, 589 and 590, 590 and 591, 591 and 592, 592 and593, 593 and 594, 594 and 595, 595 and 596, 596 and 597, 597 and 598,598 and 599, 599 and 600, 601 and 602, 602 and 603, 603 and 604, 604 and605, 605 and 606, 606 and 607, 607 and 608, 608 and 609, 609 and 610,610 and 611, 611 and 612, 612 and 613, 613 and 614, 614 and 615, 615 and616, 616 and 617, 617 and 618, 618 and 619, 619 and 620, 620 and 621,621 and 622, 622 and 623, 623 and 624, 624 and 625, 625 and 626, 626 and627, 627 and 628, 628 and 629, 629 and 630, 630 and 631, 631 and 632,632 and 633, 633 and 634, 634 and 635, 635 and 636, 636 and 637, 637 and638, 638 and 639, 639 and 640, 640 and 641, 641 and 642, 642 and 643,643 and 644, 644 and 645, 645 and 646, 646 and 647, 647 and 648, 648 and649, 649 and 650, 650 and 651, 651 and 652, 652 and 653, 653 and 654,654 and 655, 655 and 656, 656 and 657, 657 and 658, 658 and 659, 659 and660, 660 and 661, 661 and 662, 662 and 663, 663 and 664, 664 and 665,665 and 666, 666 and 667, 667 and 668, 668 and 669, 669 and 670, 670 and671, 671 and 672, 72 and 673, 673 and 674, 674 and 675, 675 and 676, 676and 677, 677 and 678, 678 and 679, 679 and 680, 680 and 681, 681 and682, 682 and 683, 683 and 684, or 684 and 685 of an NS3/4A polypeptide(e.g., SEQ ID NO: 2) or NS3/4A variant polypeptide, (e.g., SEQ ID NO:36), or fragment thereof. In preferred embodiments, the chimeric NS3/4Apolypeptides can consist of, consist essentially of, or comprise anantigen, TCE, antigen and linker, TCE and linker, antigen and adjuvantsequence, TCE and adjuvant sequence, antigen and linker and adjuvantsequence, or TCE and linker and adjuvant sequence inserted between aminoacids 453 and 513 of SEQ ID NO:36, or in an analogous position in anyNS3/4A polypeptide.

In some embodiments, the chimeric NS3/4A polypeptide includes anantigen, TCE, antigen and linker, TCE and linker, antigen and adjuvantsequence, TCE and adjuvant sequence, antigen and linker and adjuvantsequence, or TCE and linker and adjuvant sequence that is juxtaposed toor flanking the NS3/4A polypeptide or a fragment thereof. For example,the TCE can be juxtaposed to or flanking the N-terminal or C-terminalend of the chimeric NS3/4A polypeptide or NS3/4A variant. In preferredembodiments, the chimeric NS3/4A polypeptides retain NS3 proteaseactivity, and/or NS3 helicase activity.

In some embodiments, the TCE can be derived from antigens such as viralantigens, bacterial antigens, parasitic antigens, tumor antigens,allergens and toxins. For example, in some embodiments, the TCEcomprises a sequence selected from the group consisting of SEQ ID NOs:221-571 and SEQ ID NOs:809-1011 and SEQ ID NO:1014 and SEQ ID NOs:1016-1034 and SEQ ID NOs: 1146-1173 and SEQ ID NOs: 1210-1328. Inpreferred embodiments, the encoded TCE or antigen is obtained from ahepatitis virus, such as an antigen from the Hepatitis A virus (HAV),Hepatitis B virus (HBV), or HCV or HIV, flu, Birch allergens or malaria.For example, in some embodiments, the TCE comprises the amino acidsequence of SEQ ID NO:1014. Antigens and TCEs that are present onpathogens that infect domestic animals are also embodied. That is, someembodiments include veterinary preparations that comprise a NS3/4Aplatform, as described herein, and an antigen present on an animalpathogen (e.g., swine flu, avian flu, or equine flu).

Another embodiment disclosed herein includes a composition thatcomprises a recombinant peptide immunogen comprising at least oneantigen and a hepatitis C virus (HCV) NS3 protease cleavage site,wherein the HCV NS3 protease cleavage site is joined to the antigen at aposition that is not naturally occurring. In some embodiments, theantigen comprises an epitope from a plant, virus, bacteria, or a cancercell. In other embodiments, the antigen is not a peptide from HCV. Instill other embodiments, the antigenic fragment comprises an epitopefrom birch, peanut, wheat protein, a hepatitis viral protein, ahepatitis B viral protein, or hepatitis B virus core protein (HBcAg). Inother embodiments, the antigenic fragment comprises a fragment of anantigen presented in SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 andSEQ ID NOs: 1210-1328.

In some aspects, the recombinant peptide immunogen comprises a pluralityof NS3 protease cleavage sites. In some embodiments, the NS3 proteasecleavage site is chosen from the group consisting of NS3/4A, NS4A/B,NS4B/5A, and NS5A/B. In some embodiments, the HCV NS3 protease cleavagesite comprises the sequence: SADLEVVTSTWVLVGGVL (SEQ ID NO: 1340). Inother embodiments, the HCV NS3 protease cleavage site comprises thesequence: DEMEECSQHLPYIEQG (SEQ ID NO: 1341). In still otherembodiments, the HCV NS3 protease cleavage site comprises a sequencefrom the sequences presented below:

HCV Strain Amino acid SEQ name: sequence: Junction ID: H-FDA CMSADLEVVT

STWVLVGGVL NS3/4A 1342 H-AP CMSADLEVVT

STWVLVGGVL NS3/4A 1343 HCV-1 CMSADLEVVT

STWVLVGGVL NS3/4A 1344 HCV-J CMSADLEVVT

STWVLVGGVL NS3/4A 1345 HCV-BK CMSADLEVVT

STWVLVGGVL NS3/4A 1346 HC-J6 CMQADLEVMT

STWVLAGGVL NS3/4A 1347 HCV-T CMSADLEVVT

STWVLVGGVL NS3/4A 1348 HC-J8 CMQADLEIMT

SSWVLAGGVL NS3/4A 1349 HCV-JT, JT CMSAQLEVVT

STWVLVGGVL NS3/4A 1350 H-FDA YQEFDEMEEC

SQHLPYIEQG NS4A/4B 1351 H-AP YQEFDEMEEC

SQHLPYIEQG NS4A/4B 1352 HCV-1 YREFDEMEEC

SQHLPYIEQG NS4A/4B 1353 HCV-J YQEFDEMEEC

ASHLPYIEQG NS4A/4B 1354 HCV-BK YQEFDEMEEC

ASHLPYIEQG NS4A/4B 1355 HC-J1, 4 YEAFDEMEEC

ASRAALIEEG NS4A/4B 1356 HCV-T YQEFDEMEEC

ASHLPYIEQG NS4A/4B 1357 HC-J8 YQAFDEMEEC

ASKAALIEEG NS4A/4B 1358 HCV-JT, JT′ YREFDEMEEC

ASHLPYIEQG NS4A/4B 1359 H-FDA WISSECTTPC

SGSWLRDIWD NS4B/5A 1360 H-AP WISSECTTPC

SGSWLRDIWD NS4B/5A 1361 HCV-1 WISSECTTPC

SGSWLRDIWD NS4B/5A 1362 HCV-J WINEDCSTPC

SGSWLKDVWD NS4B/5A 1363 HCV-BK WINEDCSTPC

SGSWLRDVWD NS4B/5A 1364 HC-J6 WITEDCPIPC

SGSWLRDVWD NS4B/5A 1365 HCV-T WINEDCSTPC

SGSWLRDVWD NS4B/5A 1366 HC-J8 WITEDCPVPC

SGSWLQDIWD NS4B/5A 1367 HCV-JT WINEDCSTPC

SGSWLKDVWD NS4B/5A 1368 HCV-JT′ WINEDCSTPC

SGSWLRDVWD NS4B/5A 1369 H-FDA GADTEDVVCC

SMSYTWTGAL NS5A/5B 1370 H-AP GADTEDVVCC

SMSYSWTGAL NS5A/5B 1371 HCV-1 EANAEDVVCC

SMSYSWTGAL NS5A/5B 1372 HCV-J GEAGEDVVCC

SMSYTWTGAL NS5A/5B 1373 HCV-BK EEASEDVVCC

SMSYTWTGAL NS5A/5B 1374 HC-J6 SEEDDSVVCC

SMSYSWTGAL NS5A/5B 1375 HCV-T EEDGEGVICC

SMSYTWTGAL NS5A/5B 1376 HC-J8 SDQEDSVICC

SMSYSWTGAL NS5A/5B 1377 HCV-JT, JT′ GEASDDIVCC

SMSYTWTGAL NS5A/5B 1378 CONSENSUS     D    C

S CONSENSUS     E    T

A

In other aspects, the recombinant peptide immunogen comprises aplurality of antigenic fragments of a protein assembled in anon-naturally occurring order. In other aspects, the recombinant peptideimmunogen comprises a plurality of antigenic fragments of a proteinassembled in a naturally occurring order. In still other aspects, therecombinant peptide immunogen comprises a plurality of antigenicfragments from at least two different proteins assembled in anon-naturally occurring order.

In more aspects, the composition further comprises an NS3/4A peptide. Insome embodiments, the NS3/4A peptide comprises a mutation that enhancesprotease activity. In some embodiments, the mutation is selected fromthe group consisting of Tyr6Ala, Arg11Ala, Leu13Ala, Leu14Ala, Glu30Ala,Cys52Ala, Gly58Ala, Ala59Gly, Ile64Ala, Ile64Ala, Gln73Ala, Thr76Ala,Pro86Ala, Ala111Gly, Gly 122Ala, Tyr 134Ala, Lys 136Ala, Gly 141Ala,Val158Ala, Arg161Ala, Ala166Gly, and Thr177Ala. In some embodiments, theNS3/4A peptide is joined to the peptide immunogen. In some embodiments,the NS3/4A peptide is C-terminal with respect to the peptide immunogen.In other embodiments, the NS3/4A peptide is N-terminal with respect tothe peptide immunogen. In still other embodiments, the NS3/4A peptide isinserted within the peptide immunogen. In other embodiments, the peptideimmunogen is inserted within the NS3/4A peptide. In yet otherembodiments, the NS3/4A peptide is not joined to the peptide immunogen.

Another embodiment disclosed herein includes a composition thatcomprises a nucleic acid encoding a recombinant peptide immunogencomprising an antigen and a hepatitis C virus (HCV) NS3 proteasecleavage site, wherein the HCV NS3 protease cleavage site is joined tothe antigen at a position that is not naturally occurring. In someembodiments, the antigen comprises an epitope from a plant, virus,bacteria, or cancer cell. In some embodiments, the antigen is not apeptide from HCV. In some embodiments, the antigen is an antigenicfragment of a birch, peanut, wheat protein, an antigenic fragment of ahepatitis viral protein, an antigenic fragment of a hepatitis B virusprotein, an antigenic fragment of the hepatitis B virus core protein(HBcAg).

In some aspects, the recombinant peptide immunogen comprises a pluralityof NS3 protease cleavage sites. In some embodiments, the NS3 proteasecleavage site is chosen from the group consisting of NS3/4A, NS4A/B,NS4B/5A, and NS5A/B. In some embodiments, the HCV NS3 protease cleavagesite comprises the sequence: SADLEVVTSTWVLVGGVL (SEQ ID NO: 1340). Inother embodiments, the HCV NS3 protease cleavage site comprises thesequence: DMEECSQHLPYIEQG (SEQ ID NO: 1341).

In other aspects, the recombinant peptide immunogen comprises aplurality of antigenic fragments of a protein assembled in anon-naturally occurring order. In other aspects, the recombinant peptideimmunogen comprises a plurality of antigenic fragments of a proteinassembled in a naturally occurring order. In still other aspects, therecombinant peptide immunogen comprises a plurality of antigenicfragments from at least two different proteins assembled in anon-naturally occurring order. In some embodiments, a peptide immunogendescribed herein is not native to hepatitis C. In other embodiments, apeptide immunogen described herein is not native to a hepatitis virus.In other embodiments, a peptide immunogen described herein is not nativeto influenza.

In some aspects, the composition further comprises a nucleic acidencoding NS3/4A peptide. In some embodiments, the nucleic acid codingfor NS3/4A peptide is codon-optimized for expression in a mammal orbird. In other embodiments, the nucleic acid coding the NS3/4A peptideis codon-optimized for expression in a human, dog, cat, horse, pig, cow,goat, or chicken In some embodiments, the NS3/4A peptide comprises amutation that enhances protease activity. In some embodiments, themutation is selected from the group consisting of Tyr6Ala, Arg11Ala,Leu13Ala, Leu14Ala, Glu30Ala, Cys52Ala, Gly58Ala, Ala59Gly, Ile64Ala,Ile64Ala, Gln73Ala, Thr76Ala, Pro86Ala, Ala111Gly, Gly 122Ala, Tyr134Ala, Lys 136Ala, Gly 141Ala, Val158Ala, Arg161Ala, Ala166Gly, andThr177Ala. In some embodiments, the nucleic acid encoding NS3/4A peptideis joined to the nucleic acid encoding the peptide immunogen. In yetother embodiments, the nucleic acid encoding NS3/4A peptide is notjoined to the peptide immunogen.

In an alternative aspect, the composition further comprises the NS3/4Apeptide. In some embodiments, the NS3/4A peptide comprises a mutationthat enhances protease activity. In some embodiments, the mutation isselected from the group consisting of Tyr6Ala, Arg11Ala, Leu13Ala,Leu14Ala, Glu30Ala, Cys52Ala, Gly58Ala, Ala59Gly, Ile64Ala, Ile64Ala,Gln73Ala, Thr76Ala, Pro86Ala, Ala111Gly, Gly 122Ala, Tyr 134Ala, Lys136Ala, Gly 141Ala, Val158Ala, Arg161Ala, Ala166Gly, and Thr177Ala. Insome embodiment, the NS3/4A peptide is joined to the peptide immunogen.In some embodiments, the NS3/4A peptide is C-terminal with respect tothe peptide immunogen. In other embodiments, the NS3/4A peptide isN-terminal with respect to the peptide immunogen. In still otherembodiments, the NS3/4A peptide is inserted within the peptideimmunogen. In other embodiments, the peptide immunogen is insertedwithin the NS3/4A peptide. In yet other embodiments, the NS3/4A peptideis not joined to the peptide immunogen.

It has been discovered that certain mutations in the NS3 domain of HCVallow for protease cleavage of some substrates but not others. Moreparticularly, it was found that alanine substitution at positions 1050and 1060 of the NS3 protease created protease molecules with alteredsubstrate specificity. The HCV NS3 mutants V1050A and Q1060A were foundto cleave at the NS3-NS4A junction but were unable to cleave thecellular substrate IPS-1/Cardif/MAVS/VISA. Since cleavage ofIPS-1/Cardif/MAVS/VISA by wild-type NS3 reduces the response to thetoll-like receptors (TLR-3) and the RIG-1 pathway, which in turn impairsinterferon (IFN) alpha and beta signaling, it is contemplated that theHCV NS3 V1055A and Q1060A mutants allow for cleavage of the NS3-4Ajunction without reducing interferon alpha and beta signaling. Type Iinterferons are central mediators for antiviral responses.Interferon-promoter stimulator 1 (IPS-1) contains an N-terminalCARD-like structure that mediates interaction with the CARD of RIG-I andMda5, which are cytoplasmic RNA helicases that sense viral infection.‘Knockdown’ of IPS-1 by small interfering RNA blocks interferoninduction by virus infection. Thus, IPS-1 is an adaptor involved inRIG-I- and Mda5-mediated antiviral immune responses.

Accordingly, HCV NS3 mutants V1055A and Q1060A, protease activefragments of these molecules containing said mutations, and nucleicacids encoding these molecules are therefore useful in the HCV immunogenfusion proteins or vaccines described herein for induction of an immuneresponse against HCV when elevated interferon alpha and beta signaling(e.g., amounts of IFN-alpha or IFN-beta commensurate with amounts ofIFN-alpha or IFN-beta in uninfected cells or an infected individual) isdesired. Additionally, the HCV NS3 mutants V1050A and Q1060A, proteaseactive fragments of these molecules containing said mutations, andnucleic acids encoding these molecules are useful as platforms forincorporation or attachment of heterologous peptides to which an immuneresponse is desired when elevated interferon alpha and beta signaling(e.g., amounts of IFN-alpha or IFN-beta commensurate with amounts ofIFN-alpha or IFN-beta in uninfected cells or an uninfected individual)is preferred. Furthermore, HCV NS3 mutants V1050A and Q1060A, proteaseactive fragments of these molecules containing said mutations, andnucleic acids encoding these molecules can be provided in combinationwith other immunogenic peptides or nucleic acids encoding immunogenicpeptides so as induce an adjuvant activity toward said immunogenicpeptides or to otherwise induce an immune response characterized byinterferon alpha and beta signaling commensurate with that observed inuninfected cells or an uninfected individual.

Embodiments comprise, consist, or consist essentially of the peptides(SEQ. ID. NOS.:68, 73, and 1329) or fragments thereof that retainprotease activity, nucleic acids encoding these molecules, vectorshaving said nucleic acids, and cells having said vectors, nucleic acids,or peptides. Additional embodiments include an NS3 or NS3/4A encodingnucleic acid or fragment thereof or corresponding peptide, whichcomprise a sequence that was optimized for codons most frequently usedin humans. That is, more embodiments comprise, consist, or consistessentially of nucleic acids that have been codon optimized forexpression in humans, which encode the mutant HCV peptides describedherein (e.g., SEQ. ID. NOS.:68, 73, and 1329) or fragments thereof thatretain protease activity. Vectors having said codon-optimized nucleicacids, immunogenic preparations, and vaccines having saidcodon-optimized nucleic acids and vectors and cells having said vectorsare also embodiments. Preferred embodiments include DNA immunogens thatcomprise, consist, or consist essentially of nucleic acids encoding SEQ.ID. NOS 68, 73, and 1329 or a fragment thereof that retain proteaseactivity. These DNA immunogens can be provided to cells by transfection,injection, electroporation, needle electroporation (e.g., Medpulsar orElgin), gene gun, transdermal application, or intranasal application.

In one embodiment, specific mutations of the NS3 protease domain can bemade and screened to find specific mutants that have little effect, noeffect, or heightened effect on protease cleavage at the NS3-NS4acleavage site while losing the ability to cleave IPS-1 to ΔIPS-1. In apreferred embodiment, amino acids 1053 through 1062 of the NS3/4A gene,corresponding to amino acids 27 through 36 of SEQ ID NOs.:1330-1339 havebeen identified as affecting the specificity of the NS3 protease domain.Accordingly, mutations in this region of the NS3/4A or fragmentscontaining mutations in this region can be selected for their ability tocleave the NS3-NS4A cleavage site while being unable to cleave IPS-1 toΔIPS-1.

A large scale mutational analysis of HCV NS3 domain was undertaken. Thisproject produced a variety of truncated versions of the NS3/4A peptide(e.g., SEQ. ID. NOs.: 12 and 13) and mutants that lacked a proteolyticcleavage site (e.g., SEQ. ID. NOs.: 3-11). Other HCV NS3 mutants werefound to have altered protease activity (e.g., SEQ ID NOs: 40-220). Forexample, some mutants, which have an alanine substitution or a glycinesubstitution in the NS3 protease domain were found to have an abolished,reduced, enhanced, or greatly enhanced protease activity. Exemplarymutants include SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ IDNO:43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQID NO:48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52,SEQ ID NO; 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO:57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO; 61, SEQ IDNO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71,SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO:76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ IDNO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90,SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO:95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ IDNO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104,SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ IDNO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113,SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ IDNO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122,SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ IDNO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131,SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ IDNO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140,SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ IDNO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149,SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ IDNO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158,SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ IDNO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167,SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ IDNO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176,SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ IDNO: 181, SEQ ID NO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185,SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ IDNO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194,SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ IDNO: 199, SEQ ID NO: 200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 203,SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 206, SEQ ID NO: 207, SEQ IDNO: 208, SEQ ID NO: 209, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 212,SEQ ID NO: 213, SEQ ID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216, SEQ IDNO: 217, SEQ ID NO: 218, SEQ ID NO: 219, or SEQ ID NO: 220. Accordingly,regions of the NS3 domain, which retained protease activity wascarefully mapped by mutational analysis. Surprisingly, approximately 87%of the protease residues could be replaced and protease activity wasretained.

Aspects of the present invention include compositions that comprise,consist, or consist essentially of the nucleic acid sequence provided bythe sequence of SEQ. ID. NO.: 35 and/or the peptide sequence provided bythe sequence of SEQ. ID. NO.: 36. Preferred embodiments, for example,include compositions that comprise, consist or consist essentially ofany number of consecutive nucleotides between at least 12-2112nucleotides of SEQ. ID. NO.: 35 or a complement thereof (e.g., 12-15,15-20, 20-30, 30-50, 50-100, 100-200, 200-500, 500-1000, 1000-1500,1500-2079, or 1500-2112 consecutive nucleotides). Preferred embodimentsalso include compositions that comprise, consist or consist essentiallyof any number of consecutive nucleotides between at least 12-2112nucleotides of SEQ. ID. NO.: 35 or a complement thereof (e.g., at least3, 4, 6, 8, 10, 12, 15, 20, 30, 40, 50, 60, 70, 80, 90, or 100consecutive nucleotides acids of SEQ. ID. NO.: 35). Additionalembodiments include nucleic acids that comprise, consist, or consistessentially of a sequence that encodes SEQ. ID. NO.: 36 or a fragmentthereof, that is, any number of consecutive amino acids between at least3-50 amino acids of SEQ. ID. NO.: 36 (e.g., 3, 4, 6, 8, 10, 12, 15, 20,25, 30, 35, 40, 45, or 50 consecutive amino acids). Still moreembodiments include peptides that comprises, consist, or consistessentially of the sequence of SEQ. ID. NO.: 36 or a fragment thereof,that is, any number of consecutive amino acids between at least 3-50amino acids of SEQ. ID. NO.: 36 (e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25,30, 35, 40, 45, or 50 consecutive amino acids).

Other preferred embodiments include compositions that comprise, consist,or consist essentially of any number of consecutive nucleotides betweenat least 12-2112 nucleotides that encode the polypeptides of SEQ ID NO:40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO:43, SEQ ID NO: 44, SEQ IDNO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO:48, SEQ ID NO: 49, SEQID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54,SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO:59, SEQ ID NO: 60, SEQ ID NO; 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ IDNO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73,SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO:78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ IDNO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92,SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO:97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ IDNO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106,SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ IDNO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115,SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ IDNO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124,SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ IDNO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133,SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ IDNO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142,SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ IDNO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151,SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ IDNO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160,SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ IDNO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169,SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ IDNO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178,SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ IDNO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 187,SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ IDNO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196,SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 200, SEQ IDNO: 201, SEQ ID NO: 202, SEQ ID NO: 203, SEQ ID NO: 204, SEQ ID NO: 205,SEQ ID NO: 206, SEQ ID NO: 207, SEQ ID NO: 208, SEQ ID NO: 209, SEQ IDNO: 210, SEQ ID NO: 211, SEQ ID NO: 212, SEQ ID NO: 213, SEQ ID NO: 214,SEQ ID NO: 215, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 218, SEQ IDNO: 219, or SEQ ID NO: 220, wherein the nucleic acid includes the codingsequence for the mutation in the NS3 protease domain of the aboveNS3/NS4A polypeptides, or a complement thereof, (e.g., 12-15, 15-20,20-30, 30-50, 50-100, 100-200, 200-500, 500-1000, 1000-1500, 1500-2079,or 1500-2112 consecutive nucleotides).

Methods of making and using the compositions described herein are alsoprovided. In addition to methods of making the embodied nucleic acidsand peptides, other embodiments include methods of making immunogensand/or vaccine compositions that can be used to treat or prevent HCVinfection. Some methods are practiced, for example, by mixing anadjuvant with a peptide or nucleic acid antigen (e.g., an HCV peptide orHCV nucleic acid), as described above, so as to formulate a singlecomposition (e.g., a vaccine composition). Preferred methods involve themixing of ribavirin with an HCV gene or antigen disclosed herein.

Preferred methods of using the compositions described herein involveproviding an animal in need of an immune response to HCV with asufficient amount of one or more of the nucleic acid or peptideembodiments described herein. By one approach, for example, an animal inneed of an immune response to HCV (e.g., an animal at risk or alreadyinfected with HCV, such as a human) is identified and said animal isprovided an amount of NS3/4A (SEQ. ID. NO.: 2 or SEQ. ID. NO.: 36), amutant NS3/4A (SEQ. ID. NOs.: 3-13), a fragment thereof (e.g., SEQ. ID.NOs.: 14-26) or a nucleic acid encoding said molecules that is effectiveto enhance or facilitate an immune response to the hepatitis viralantigen. Additional methods are practiced by identifying an animal inneed of a potent immune response to HCV and providing said animal acomposition comprising a peptide comprising an antigen or epitopepresent on SEQ. ID. NOs.: 2-27 or SEQ. ID. NO.: 36 or a nucleic acidencoding said peptides. Particularly preferred methods involve theidentification of an animal in need of an immune response to HCV andproviding said animal a composition comprising an amount of HCV antigen(e.g., NS3/4A (SEQ. ID. NO.: 2 or SEQ. ID. NO.: 36)), mutant NS3/4A(SEQ. ID. NOs.: 3-13), a fragment thereof containing any number ofconsecutive amino acids between at least 3-50 amino acids (e.g., 3, 4,6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, or 50 consecutive amino acids)of SEQ. ID. NO.: 2 or SEQ. ID. NO.: 36 (e.g., SEQ. ID. NOs.: 14-26) or anucleic acid encoding one or more of these molecules that is sufficientto enhance or facilitate an immune response to said antigen. In someembodiments, the composition described above also contains an amount ofribavirin that provides an adjuvant effect.

Other approaches concern identifying an animal in need of an immuneresponse to HCV and providing an amount of NS3/4A polypeptides withaltered protease activity, or mutations in the NS3 protease domain(e.g., SEQ. ID. NO SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ IDNO:43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQID NO:48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52,SEQ ID NO; 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO:57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO; 61, SEQ IDNO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71,SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO:76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ IDNO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90,SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO:95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ IDNO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104,SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ IDNO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113,SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ IDNO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122,SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ IDNO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131,SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ IDNO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140,SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ IDNO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149,SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ IDNO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158,SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ IDNO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167,SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ IDNO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176,SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ IDNO: 181, SEQ ID NO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185,SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ IDNO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194,SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ IDNO: 199, SEQ ID NO: 200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 203,SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 206, SEQ ID NO: 207, SEQ IDNO: 208, SEQ ID NO: 209, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 212,SEQ ID NO: 213, SEQ ID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216, SEQ IDNO: 217, SEQ ID NO: 218, SEQ ID NO: 219, or SEQ ID NO: 220, a fragmentthereof, or a nucleic acid encoding said molecules that is effective toenhance or facilitate an immune response to the hepatitis viral antigen.Additional methods are practiced by identifying an animal in need of apotent immune response to HCV and providing said animal a compositioncomprising a peptide comprising an antigen or epitope present on SEQ.ID. NO SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO:43, SEQ IDNO: 44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO:48, SEQID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO; 53,SEQ ID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO:58, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO; 61, SEQ ID NO: 62, SEQ IDNO: 63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72,SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO:77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ IDNO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQID NO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91,SEQ ID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO:96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ IDNO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105,SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ IDNO: 110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114,SEQ ID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ IDNO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123,SEQ ID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ IDNO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132,SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ IDNO: 137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141,SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ IDNO: 146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150,SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ IDNO: 155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159,SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ IDNO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168,SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ IDNO: 173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177,SEQ ID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ IDNO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186,SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ IDNO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195,SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199, SEQ IDNO: 200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 203, SEQ ID NO: 204,SEQ ID NO: 205, SEQ ID NO: 206, SEQ ID NO: 207, SEQ ID NO: 208, SEQ IDNO: 209, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 212, SEQ ID NO: 213,SEQ ID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216, SEQ ID NO: 217, SEQ IDNO: 218, SEQ ID NO: 219, or SEQ ID NO: 220 or a nucleic acid encodingsaid peptides. Particularly preferred methods involve the identificationof an animal in need of an immune response to HCV and providing saidanimal a composition comprising an amount of HCV antigen (e.g. SEQ. ID.NO SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO:48, SEQ IDNO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO; 53, SEQID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58,SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO; 61, SEQ ID NO: 62, SEQ ID NO:63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ IDNO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77,SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO:82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ IDNO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96,SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO:101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO:110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO:119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO:128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO:137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO:146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO:155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO:164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO:173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO:182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO:191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO:200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 203, SEQ ID NO: 204, SEQID NO: 205, SEQ ID NO: 206, SEQ ID NO: 207, SEQ ID NO: 208, SEQ ID NO:209, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 212, SEQ ID NO: 213, SEQID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO:218, SEQ ID NO: 219, SEQ ID NO: 220), a fragment thereof containing anynumber of consecutive amino acids between at least 3-50 amino acids,wherein the fragment includes the mutation in the NS3 protease domain,(e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, or 50 consecutiveamino acids), or a nucleic acid encoding one or more of these moleculesthat is sufficient to enhance or facilitate an immune response to saidantigen. In some embodiments, the composition described above alsocontains an amount of ribavirin that provides an adjuvant effect.

In still more embodiments, for example, a gene gun is used to administeran HCV nucleic acid described herein (e.g., SEQ. ID. NO.: 35 or fragmentthereof, as described above) to a mammalian subject in need of an immuneresponse to HCV. In some embodiments, an amount of ribavirin is mixedwith the DNA immunogen prior to delivery with the gene gun. In otherembodiments, the DNA immunogen is provided by gene gun shortly before orafter administration of ribavirin at or near the same site of DNAinoculation. For example, in some embodiments, a gene gun or atransdermal delivery system is used to administer HCV nucleic acidsincluding nucleic acids encoding the NS3/NS4A polypeptides with alteredprotease activity. Accordingly, a gene gun or a transdermal deliverysystem is used to deliver nucleotides encoding the NS3/NS4A polypeptidesof SEQ ID NO: 40, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO:43, SEQ ID NO:44, SEQ ID NO: 45, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO:48, SEQ IDNO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO; 53, SEQID NO: 54, SEQ ID NO: 55, SEQ ID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58,SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO; 61, SEQ ID NO: 62, SEQ ID NO:63, SEQ ID NO: 64, SEQ ID NO: 65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ IDNO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQID NO: 73, SEQ ID NO: 74, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77,SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO:82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ IDNO: 87, SEQ ID NO: 88, SEQ ID NO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQID NO: 92, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96,SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO:101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO:110, SEQ ID NO: 111, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQID NO: 115, SEQ ID NO: 116, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO:119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQID NO: 124, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO:128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO:137, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO:146, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO:155, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO:164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQID NO: 169, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO:173, SEQ ID NO: 174, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQID NO: 178, SEQ ID NO: 179, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO:182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO:191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO:200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 203, SEQ ID NO: 204, SEQID NO: 205, SEQ ID NO: 206, SEQ ID NO: 207, SEQ ID NO: 208, SEQ ID NO:209, SEQ ID NO: 210, SEQ ID NO: 211, SEQ ID NO: 212, SEQ ID NO: 213, SEQID NO: 214, SEQ ID NO: 215, SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO:218, SEQ ID NO: 219, and SEQ ID NO: 220, or fragments thereof thatcontain the mutation in the NS3 protease domain, either with or withoutribavirin.

In still other embodiments, transdermal delivery systems are used todeliver an HCV polypeptide described herein to a mammalian subject inneed of an immune response to HCV. In some embodiments, an amount ofribavirin is mixed and delivered transdermally with the HCV polypeptide.In other embodiments, an amount of ribavirin is transdermally deliveredto a mammal shortly before or shortly after transdermal delivery of theHCV polypeptide, at or near the same site as the polypeptide. Forexample, embodiments include transdermal delivery of NS3/NS4Apolypeptides having altered protease activity. Thus, in someembodiments, the NS3/NS4A polypeptides of SEQ ID NO: 40, SEQ ID NO: 41,SEQ ID NO: 42, SEQ ID NO:43, SEQ ID NO: 44, SEQ ID NO: 45, SEQ ID NO:46, SEQ ID NO: 47, SEQ ID NO:48, SEQ ID NO: 49, SEQ ID NO: 50, SEQ IDNO: 51, SEQ ID NO: 52, SEQ ID NO; 53, SEQ ID NO: 54, SEQ ID NO: 55, SEQID NO: 56, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 59, SEQ ID NO: 60,SEQ ID NO; 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO:65, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ IDNO: 70, SEQ ID NO: 71, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79,SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO:84, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 87, SEQ ID NO: 88, SEQ IDNO: 89, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 93, SEQID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98,SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ IDNO: 103, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107,SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ IDNO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 116,SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ IDNO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 125,SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ IDNO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134,SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ IDNO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143,SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 147, SEQ IDNO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152,SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 156, SEQ IDNO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161,SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ IDNO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170,SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 174, SEQ IDNO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 179,SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 183, SEQ IDNO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188,SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ IDNO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197,SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 200, SEQ ID NO: 201, SEQ IDNO: 202, SEQ ID NO: 203, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 206,SEQ ID NO: 207, SEQ ID NO: 208, SEQ ID NO: 209, SEQ ID NO: 210, SEQ IDNO: 211, SEQ ID NO: 212, SEQ ID NO: 213, SEQ ID NO: 214, SEQ ID NO: 215,SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 218, SEQ ID NO: 219, and SEQID NO: 220 are delivered transdermally to a mammalian subject in need ofan immune response to HCV, either with or without ribavirin.

Some embodiments relate to methods of inducing an immune response toHepatitis C Virus using any of the peptides, nucleic acids, nucleicacids encoding said peptides, peptide fragments, or nucleic acidsencoding said peptide fragments described herein.

Other embodiments relate to methods of inducing an immune response toheterologous antigen joined to or co-administered with the peptides,nucleic acids, nucleic acids encoding said peptides, peptide fragments,or nucleic acids encoding said peptide fragments described herein. Insome aspects the heterologous antigen is chemically fused to thepeptides, nucleic acids, nucleic acids encoding said peptides, peptidefragments, or nucleic acids encoding said peptide fragments describedherein. In other aspects the heterologous antigen is co-administered tothe peptides, nucleic acids, nucleic acids encoding said peptides,peptide fragments, or nucleic acids encoding said peptide fragmentsdescribed herein. In still other aspects the heterologous antigen isadministered before administration of the peptides, nucleic acids,nucleic acids encoding said peptides, peptide fragments, or nucleicacids encoding said peptide fragments described herein. In other aspectsthe heterologous antigen is administered after administration of thepeptides, nucleic acids, nucleic acids encoding said peptides, peptidefragments, or nucleic acids encoding said peptide fragments describedherein.

In some aspects, nucleic acids encoding heterologous antigens describedherein that are joined to or co-administered with the nucleic acids,nucleic acids encoding said peptides, peptide fragments, or nucleicacids encoding said peptide fragments described herein are at least, atleast about, less than, or less than about 3 nucleotides, 4 nucleotides,5 nucleotides, 6 nucleotides, 7 nucleotides, 8 nucleotides, 9nucleotides, 10 nucleotides, 11 nucleotides, 12 nucleotides, 13nucleotides, 14 nucleotides, 15 nucleotides, 16 nucleotides, 17nucleotides, 18 nucleotides, 19 nucleotides, 20 nucleotides, 21nucleotides, 22 nucleotides, 23 nucleotides, 24 nucleotides, 25nucleotides, 26 nucleotides, 27 nucleotides, 28 nucleotides, 29nucleotides, 30 nucleotides, 31 nucleotides, 32 nucleotides, 33nucleotides, 34 nucleotides, 35 nucleotides, 36 nucleotides, 37nucleotides, 38 nucleotides, 39 nucleotides, 40 nucleotides, 41nucleotides, 42 nucleotides, 43 nucleotides, 44 nucleotides, 45nucleotides, 46 nucleotides, 47 nucleotides, 48 nucleotides, 49nucleotides, 50 nucleotides, 55 nucleotides, 60 nucleotides, 65nucleotides, 70 nucleotides, 75 nucleotides, 80 nucleotides, 85nucleotides, 90 nucleotides, 95 nucleotides, 100 nucleotides, 110nucleotides, 120 nucleotides, 130 nucleotides, 140 nucleotides, 150nucleotides, 160 nucleotides, 170 nucleotides, 180 nucleotides, 190nucleotides, 200 nucleotides, 250 nucleotides, 300 nucleotides, 350nucleotides, 400 nucleotides, 450 nucleotides, 500 nucleotides, 550nucleotides, 600 nucleotides, 650 nucleotides, 700 nucleotides, 750nucleotides, 800 nucleotides, 850 nucleotides, 900 nucleotides, 950nucleotides, 1000 nucleotides, 1100 nucleotides, 1200 nucleotides, 1300nucleotides, 1400 nucleotides, 1500 nucleotides, 1600 nucleotides, 1700nucleotides, 1800 nucleotides, 1900 nucleotides, 2000 nucleotides, 2500nucleotides, 3000 nucleotides, 3500 nucleotides, 4000 nucleotides, 4500nucleotides, 5000 nucleotides, 6000 nucleotides, 7000 nucleotides, 8000nucleotides, 9000 nucleotides, 10,000 nucleotides in length.

In some aspects, heterologous antigens described herein that are joinedto or co-administered with the nucleic acids, nucleic acids encodingsaid peptides, peptide fragments, or nucleic acids encoding said peptidefragments described herein are at least, at least about, less than, orless than about 3 amino acids, 4 amino acids, 5 amino acids, 6 aminoacids, 7 amino acids, 8 amino acids, 9 amino acids, 10 amino acids, 11amino acids, 12 amino acids, 13 amino acids, 14 amino acids, 15 aminoacids, 16 amino acids, 17 amino acids, 18 amino acids, 19 amino acids,20 amino acids, 21 amino acids, 22 amino acids, 23 amino acids, 24 aminoacids, 25 amino acids, 26 amino acids, 27 amino acids, 28 amino acids,29 amino acids, 30 amino acids, 31 amino acids, 32 amino acids, 33 aminoacids, 34 amino acids, 35 amino acids, 36 amino acids, 37 amino acids,38 amino acids, 39 amino acids, 40 amino acids, 41 amino acids, 42 aminoacids, 43 amino acids, 44 amino acids, 45 amino acids, 46 amino acids,47 amino acids, 48 amino acids, 49 amino acids, 50 amino acids, 55 aminoacids, 60 amino acids, 65 amino acids, 70 amino acids, 75 amino acids,80 amino acids, 85 amino acids, 90 amino acids, 95 amino acids, 100amino acids, 110 amino acids, 120 amino acids, 130 amino acids, 140amino acids, 150 amino acids, 160 amino acids, 170 amino acids, 180amino acids, 190 amino acids, 200 amino acids, 250 amino acids, 300amino acids, 350 amino acids, 400 amino acids, 450 amino acids, 500amino acids, 550 amino acids, 600 amino acids, 650 amino acids, 700amino acids, 750 amino acids, 800 amino acids, 850 amino acids, 900amino acids, 950 amino acids, 1000 amino acids, 1100 amino acids, 1200amino acids, 1300 amino acids, 1400 amino acids, 1500 amino acids, 1600amino acids, 1700 amino acids, 1800 amino acids, 1900 amino acids, 2000amino acids, 2500 amino acids, 3000 amino acids, 3500 amino acids, 4000amino acids, 4500 amino acids, 5000 amino acids, 6000 amino acids, 7000amino acids, 8000 amino acids, 9000 amino acids, 10,000 amino acids inlength.

Still other embodiments relate to methods of inducing an immune responseas described herein when cleavage of IPS-1 to Δ IPS-1 is not desired.

Other embodiments relate to methods of inducing an immune response asdescribed herein wherein repression of IFNα and/or IFNβ is not desired.This is particularly useful when raising an immune response to HCVbecause HCV NS3/4A represses IFNα and IFNβ expression throughproteolytic cleavage of IPS-1.

One embodiment relates to a method of enhancing an immune response to ahepatitis C antigen comprising identifying an animal in need of anenhanced immune response to a hepatitis C antigen and providing to saidanimal a composition comprising a nucleic acid sequence that encodes apeptide comprising an NS3 protease domain that cleaves NS3-NS4A cleavagesite but does not cleave IPS-1 to ΔIPS-1.

Another embodiment relates to a method of enhancing an immune responseto a hepatitis C antigen comprising identifying an animal in need of anenhanced immune response to a hepatitis C antigen and providing to saidanimal a peptide that comprises an NS3 protease domain that cleavesNS3-NS4A cleavage site but does not cleave IPS-1 to ΔIPS-1. In oneaspect of the embodiments, the composition further comprises ribavirin.In another aspect of the embodiments, the peptide used is selected fromthe group consisting of SEQ ID NO: 68, SEQ ID NO: 73, SEQ ID NO: 1329,SEQ ID NO: 1330, SEQ ID NO: 1331, SEQ ID NO: 1332, SEQ ID NO: 1333, SEQID NO: 1334, SEQ ID NO: 1335, SEQ ID NO: 1336, SEQ ID NO: 1337, SEQ IDNO: 1338, and SEQ ID NO: 1339.

Another embodiment relates to a method of enhancing an immune responseto a hepatitis C antigen comprising identifying an animal in need of anenhanced immune response to a hepatitis C antigen and providing to saidanimal a composition comprising at least 100 consecutive nucleotides ofa nucleic acid sequence that encodes a peptide comprising an NS3protease domain that cleaves NS3-NS4A cleavage site but does not cleaveIPS-1 to ΔIPS-1, wherein said nucleic acid codes for a peptide fragmentthat retains the ability to cleave the NS3-NS4A cleavage site but notcleave IPS-1 to ΔIPS-1.

Still another embodiment relates to a method of enhancing an immuneresponse to a hepatitis C antigen comprising identifying an animal inneed of an enhanced immune response to a hepatitis C antigen andproviding to said animal a composition comprising a peptide comprisingat least 34 amino acids of an NS3 protease domain that cleaves NS3-NS4Acleavage site but does not cleave IPS-1 to ΔIPS-1, wherein said peptidefragment retains the ability to cleave the NS3-NS4A cleavage site butnot cleave IPS-1 to ΔIPS-1.

One embodiments relates to a purified or isolated nucleic acid encodinga polypeptide comprising an NS3/NS4A polypeptide that cleaves NS3-NS4Acleavage site but cannot cleave IPS-1 to ΔIPS-1 wherein the polypeptideis SEQ ID NO. 1329.

In one aspect, the mutant NS3/4A peptide has altered cleavagespecificity for host proteins. In another aspect, the nucleic acid ispart of a composition. In some aspects, the composition furthercomprises ribavirin.

One embodiment relates to a purified or isolated nucleic acid encoding amutant NS/4A peptide with retained protease activity, wherein saidmutant NS3/4A peptide has altered cleavage specificity for hostproteins.

One embodiment relates to a method of enhancing an immune response to ahepatitis C antigen comprising identifying an animal in need of anenhanced immune response to a hepatitis C antigen; and administering tosaid animal a composition a purified or isolated nucleic acid encoding amutant NS/4A peptide with retained protease activity, wherein saidmutant NS3/4A peptide has altered cleavage specificity for hostproteins. In one aspect, the composition further comprises ribavirin. Inanother aspect of the method, ribavirin is co-administered. In yetanother aspect, the co-administration of ribavirin is immediately beforeor immediately after the administration of said composition. In yetanother aspect of the embodiments described herein, the site of saidadministration, or a region proximal to said site of administration, iscontacted with an electrode configured for electroporation of a nucleicacid.

Vectors that include the isolated nucleic acids or that encode theisolated polypeptides described herein are also embodiments.Compositions that include the nucleic acids, polypeptides, and vectorsdescribed herein (e.g., vials, tubes, hypodermic needles,electroporation devices, oils, and transdermal delivery compositions)are also embodiments. Cells that include these vectors are also providedherein. For example, in some embodiments, the nucleic acids describedherein are inserted into an expression vector such as a pVAX™ expressionvector or are inserted into a Semliki forest virus vector and theseexpression constructs are provided to a subject in need of an immuneresponse to the antigen.

Stated differently, several embodiments described herein concern nucleicacids that encode a recombinant HCV NS3/4A chimeric molecule, whereinthe nucleic acid encodes four domains (domain W, domain X, domain Y, anddomain Z). Domain W can encode an NS3 protease domain prepared asdescribed herein (e.g., a mutant or modified version), or fragmentthereof, domain X can encode an NS3 helicase domain, or a fragmentthereof, and domain Y can encode an NS4A co-factor domain, or a fragmentthereof. Domain Z can encode an antigen, an epitope of a pathogen, aTCE, and/or the aforementioned molecules with or without a linker and/oradjuvant sequence. In preferred embodiments, the recombinant HCV NS3/4Achimeric polypeptide retains catalytic activity (e.g., protease,helicase, or protease and helicase activity). In preferred embodiments,domain Z is in a position within the recombinant nucleic acid andencoded chimeric polypeptide, which is non-naturally-occurring (e.g.,when Z encodes an HCV antigen).

In some embodiments, the W domain comprises the nucleic acid sequence ofresidues 1-551 of an NS3/4A sequence such as SEQ ID NOs: 1 or 35, or ananalogous sequence of any NS3/4A nucleic acid, or a fragment thereof(e.g., said fragment can comprise, consist of, or consist essentially ofabout at least, equal to, greater than, less than, or any number inbetween 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300consecutive nucleotides of the protease domain of SEQ. ID. Nos. 1 or35). In some embodiments, the X domain can comprise the nucleic acidsequence of residues 218-1568 of SEQ ID NOs: 1 or 35, or an analogoussequence of any NS3/4A nucleic acid, or a fragment thereof (e.g., saidfragment can comprise, consist of, or consist essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the helicase domain of SEQ. ID. Nos. 1 or 35). In someembodiments, the Y domain can comprise the nucleic acid sequence ofresidues 1569-2069 of SEQ ID NOs: 1 or 35, or an analogous sequence ofany NS3/4A nucleic acid, or a fragment thereof (e.g., said fragment cancomprise, consist of, or consist essentially of about at least, equalto, greater than, less than, or any number in between 9, 15, 30, 50, 75,100, 125, 150, 175, 200, 250, 300, or 350 consecutive nucleotides of theNS4A domain of SEQ. ID. Nos. 1 or 35). In preferred embodiments, the Zdomain can comprise the nucleic acid sequence of an antigen, preferablya TCE, and more preferably a sequence selected from the group consistingof SEQ ID NOs: 221-571 and SEQ ID NOs:809-1011 and SEQ ID NO:1014.

In some embodiments, the Z domain is located within or flanking (e.g.,juxtaposed or immediately adjacent to) said W domain. For example, thenucleic acid encoding the Z domain can place the encoded antigen betweenor next to amino acids 1 and 2, 2 and 3, 3 and 4, 4 and 5, 5 and 6, 6and 7, 7 and 8, 8 and 9, 9 and 10, 10 and 11, 11 and 12, 12 and 13, 13and 14, 14 and 15, 15 and 16, 16 and 17, 17 and 18, 18 and 19, 19 and20, 20 and 21, 21 and 22, 22 and 23, 23 and 24, 24 and 25, 25 and 26, 26and 27, 27 and 28, 28 and 29, 29 and 30, 30 and 31, 31 and 32, 32 and33, 33 and 34, 34 and 35, 35 and 36, 36 and 37, 37 and 38, 38 and 39, 39and 40, 40 and 41, 41 and 42, 42 and 43, 43 and 44, 44 and 45, 45 and46, 46 and 47, 47 and 48, 48 and 49, 49 and 50, 50 and 51, 51 and 52, 52and 53, 53 and 54, 54 and 55, 55 and 56, 56 and 57, 57 and 58, 58 and59, 59 and 60, 60 and 61, 61 and 62, 62 and 63, 63 and 64, 64 and 65, 65and 66, 66 and 67, 67 and 68, 68 and 69, 69 and 70, 70 and 71, 71 and72, 72 and 73, 73 and 74, 74 and 75, 75 and 76, 76 and 77, 77 and 78, 78and 79, 79 and 80, 80 and 81, 81 and 82, 82 and 83, 83 and 84, 84 and85, 85 and 86, 86 and 87, 87 and 88, 88 and 89, 89 and 90, 90 and 91, 91and 92, 92 and 93, 93 and 94, 94 and 95, 95 and 96, 96 and 97, 97 and98, 98 and 99, 99 and 100, 100 and 101, 101 and 102, 102 and 103, 103and 104, 104 and 105, 105 and 106, 106 and 107, 107 and 108, 108 and109, 109 and 110, 110 and 111, 111 and 112, 112 and 113, 113 and 114,114 and 115, 115 and 116, 116 and 117, 117 and 118, 118 and 119, 119 and120, 120 and 121, 121 and 122, 122 and 123, 123 and 124, 124 and 125,125 and 126, 126 and 127, 127 and 128, 128 and 129, 129 and 130, 130 and131, 131 and 132, 132 and 133, 133 and 134, 134 and 135, 135 and 136,136 and 137, 137 and 138, 138 and 139, 139 and 140, 140 and 141, 141 and142, 142 and 143, 143 and 144, 144 and 145, 145 and 146, 146 and 147,147 and 148, 148 and 149, 149 and 150, 150 and 151, 151 and 152, 152 and153, 153 and 154, 154 and 155, 155 and 156, 156 and 157, 157 and 158,158 and 159, 159 and 160, 160 and 161, 161 and 162, 162 and 163, 163 and164, 164 and 165, 165 and 166, 166 and 167, 167 and 168, 168 and 169,169 and 170, 170 and 171, 171 and 172, 172 and 173, 173 and 174, 174 and175, 175 and 176, 176 and 177, 177 and 178, 178 and 179, 179 and 180, or180 and 181 of said W domain of said chimeric polypeptide.

In some embodiments, the Z domain is located within or flanking (e.g.,juxtaposed or immediately adjacent to) the X domain. For example, the Zdomain can place the encoded antigen between or next to amino acids 1and 2, 2 and 3, 3 and 4, 4 and 5, 5 and 6, 6 and 7, 7 and 8, 8 and 9, 9and 10, 10 and 11, 11 and 12, 12 and 13, 13 and 14, 14 and 15, 15 and16, 16 and 17, 17 and 18, 18 and 19, 19 and 20, 20 and 21, 21 and 22, 22and 23, 23 and 24, 24 and 25, 25 and 26, 26 and 27, 27 and 28, 28 and29, 29 and 30, 30 and 31, 31 and 32, 32 and 33, 33 and 34, 34 and 35, 35and 36, 36 and 37, 37 and 38, 38 and 39, 39 and 40, 40 and 41, 41 and42, 42 and 43, 43 and 44, 44 and 45, 45 and 46, 46 and 47, 47 and 48, 48and 49, 49 and 50, 50 and 51, 51 and 52, 52 and 53, 53 and 54, 54 and55, 55 and 56, 56 and 57, 57 and 58, 58 and 59, 59 and 60, 60 and 61, 61and 62, 62 and 63, 63 and 64, 64 and 65, 65 and 66, 66 and 67, 67 and68, 68 and 69, 69 and 70, 70 and 71, 71 and 72, 72 and 73, 73 and 74, 74and 75, 75 and 76, 76 and 77, 77 and 78, 78 and 79, 79 and 80, 80 and81, 81 and 82, 82 and 83, 83 and 84, 84 and 85, 85 and 86, 86 and 87, 87and 88, 88 and 89, 89 and 90, 90 and 91, 91 and 92, 92 and 93, 93 and94, 94 and 95, 95 and 96, 96 and 97, 97 and 98, 98 and 99, 99 and 100,100 and 101, 101 and 102, 102 and 103, 103 and 104, 104 and 105, 105 and106, 106 and 107, 107 and 108, 108 and 109, 109 and 110, 110 and 111,111 and 112, 112 and 113, 113 and 114, 114 and 115, 115 and 116, 116 and117, 117 and 118, 118 and 119, 119 and 120, 120 and 121, 121 and 122,122 and 123, 123 and 124, 124 and 125, 125 and 126, 126 and 127, 127 and128, 128 and 129, 129 and 130, 130 and 131, 131 and 132, 132 and 133,133 and 134, 134 and 135, 135 and 136, 136 and 137, 137 and 138, 138 and139, 139 and 140, 140 and 141, 141 and 142, 142 and 143, 143 and 144,144 and 145, 145 and 146, 146 and 147, 147 and 148, 148 and 149, 149 and150, 150 and 151, 151 and 152, 152 and 153, 153 and 154, 154 and 155,155 and 156, 156 and 157, 157 and 158, 158 and 159, 159 and 160, 160 and161, 161 and 162, 162 and 163, 163 and 164, 164 and 165, 165 and 166,166 and 167, 167 and 168, 168 and 169, 169 and 170, 170 and 171, 171 and172, 172 and 173, 173 and 174, 174 and 175, 175 and 176, 176 and 177,177 and 178, 178 and 179, 179 and 180, 180 and 181, 181 and 182, 182 and183, 183 and 184, 184 and 185, 185 and 186, 186 and 187, 187 and 188,188 and 189, 189 and 190, 190 and 191, 191 and 192, 192 and 193, 193 and194, 194 and 195, 195 and 196, 196 and 197, 197 and 198, 198 and 199,199 and 200, 200 and 201, 201 and 202, 202 and 203, 203 and 204, 204 and205, 205 and 206, 206 and 207, 207 and 208, 208 and 209, 209 and 210,210 and 211, 211 and 212, 212 and 213, 213 and 214, 214 and 215, 215 and216, 216 and 217, 217 and 218, 218 and 219, 219 and 220, 220 and 221,221 and 222, 222 and 223, 223 and 224, 224 and 225, 225, and 226, 226and 227, 227 and 228, 228 and 229, 229 and 230, 230 and 231, 231 and232, 232 and 233, 233 and 234, 234 and 235, 235 and 236, 236 and 237,237 and 238, 238 and 239, 239 and 240, 240 and 241, 241 and 242, 242 and243, 243 and 244, 244 and 245, 245 and 246, 246 and 247, 247 and 248,248 and 249, 249 and 250, 250 and 251, 251 and 252, 252 and 253, 253 and254, 254 and 255, 255 and 256, 256 and 257, 257 and 258, 258 and 259,259 and 260, 260 and 261, 261 and 262, 262 and 263, 263 and 264, 264 and265, 265 and 266, 266 and 267, 267 and 268, 268 and 269, 269 and 270,270 and 271, 271 and 272, 272 and 273, 273 and 274, 274 and 275, 275 and276, 276 and 277, 277 and 278, 278 and 279, 279 and 280, 280 and 281,281 and 282, 282 and 283, 283 and 284, 284 and 285, 285 and 286, 286 and287, 287 and 288, 288 and 289, 289 and 290, 290 and 291, 291 and 292,292 and 293, 293 and 294, 294 and 295, 295 and 296, 296 and 297, 297 and298, 298 and 299, 299 and 300, 300 and 201, 301 and 302, 302 and 303,303 and 304, 304 and 305, 305 and 306, 306 and 307, 307 and 308, 308 and309, 309 and 310, 310 and 311, 311 and 312, 312 and 313, 313 and 314,314 and 315, 315 and 316, 316 and 317, 317 and 318, 318 and 319, 319 and320, 320 and 321, 321, and 322, 322 and 323, 323 and 324, 324 and 325,325, and 326, 326 and 327, 327 and 328, 328 and 329, 329 and 330, 330and 331, 331 and 332, 332 and 333, 333 and 334, 334 and 335, 335 and336, 336 and 337, 337 and 338, 338 and 339, 339 and 340, 340 and 341,341 and 342, 342 and 343, 343 and 344, 344 and 345, 345 and 346, 346 and347, 347 and 348, 348 and 349, 349 and 350, 350 and 351, 351 and 352,352 and 353, 353 and 354, 354 and 355, 355 and 356, 356 and 357, 357 and358, 358 and 359, 359 and 360, 360 and 361, 361 and 362, 362 and 363,363 and 364, 364 and 365, 365 and 366, 366 and 367, 367 and 368, 368 and369, 369 and 370, 370 and 371, 371 and 372, 372 and 373, 373 and 374,374 and 375, 375 and 376, 376 and 377, 377 and 378, 378 and 379, 379 and380, 380 and 381, 381 and 382, 382 and 383, 383 and 384, 384 and 385,385 and 386, 386 and 387, 387 and 388, 388 and 389, 389 and 390, 390 and391, 391 and 392, 392 and 393, 393 and 394, 394 and 395, 395 and 396,396 and 397, 397 and 398, 398 and 399, 399 and 400, 401 and 402, 402 and403, 403 and 404, 404 and 405, 405 and 406, 406 and 407, 407 and 408,408 and 409, 409 and 410, 410 and 411, 411 and 412, 412 and 413, 413 and414, 414 and 415, 415 and 416, 416 and 417, 417 and 418, 418 and 419,419 and 420, 420 and 421, 421 and 422, 422 and 423, 423 and 424, 424 and425, 425 and 426, 426 and 427, 427 and 428, 428 and 429, 429 and 430,430 and 431, 431 and 432, 432 and 433, 433 and 434, 434 and 435, 435 and436, 436 and 437, 437 and 438, 438 and 439, 439 and 440, 440 and 441,441 and 442, 442 and 443, 443 and 444, 444 and 445, 445 and 446, 446 and447, 447 and 448, 448 and 449, or 449 and 450 of the X domain of thechimeric polypeptide. Preferably, the Z domain is located between aminoacids 383 and 450 of said X domain.

Optionally, the Z domain is located within or flanking (e.g., juxtaposedor immediately adjacent to) said Y domain. For example, the Z domain canplace the encoded antigen between or next to amino acids 1 and 2, 2 and3, 3 and 4, 4 and 5, 5 and 6, 6 and 7, 7 and 8, 8 and 9, 9 and 10, 10and 11, 11 and 12, 12 and 13, 13 and 14, 14 and 15, 15 and 16, 16 and17, 17 and 18, 18 and 19, 19 and 20, 20 and 21, 21 and 22, 22 and 23, 23and 24, 24 and 25, 25 and 26, 26 and 27, 27 and 28, 28 and 29, 29 and30, 30 and 31, 31 and 32, 32 and 33, 33 and 34, 34 and 35, 35 and 36, 36and 37, 37 and 38, 38 and 39, 39 and 40, 40 and 41, 41 and 42, 42 and43, 43 and 44, 44 and 45, 45 and 46, 46 and 47, 47 and 48, 48 and 49, 49and 50, 50 and 51, 51 and 52, 52 and 53, or 53 and 54 of the Y domain ofthe chimeric polypeptide.

That is, aspects of the invention concern a composition that comprises,consists of, or consists essentially of an isolated nucleic acidprovided by the formula:

WXYZ

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid); and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

-   -   with the proviso that Z is not in a position that is naturally        occurring in HCV (e.g., when Z is an HCV antigen, the antigen is        inserted at a position that is not naturally occurring in HCV).

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated nucleic acidprovided by the formula:

ZWXY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid); and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

-   -   with the proviso that Z is not in a position that is naturally        occurring in HCV (e.g., when Z is an HCV antigen, the antigen is        inserted at a position that is not naturally occurring in HCV).

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated nucleic acidprovided by the formula:

WZXY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid); and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

with the proviso that Z is not in a position that is naturally occurringin HCV (e.g., when Z is an HCV antigen, the antigen is inserted at aposition that is not naturally occurring in HCV).

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated nucleic acidprovided by the formula:

WZXY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid); and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328)

-   -   with the proviso that Z is not in a position that is naturally        occurring in HCV (e.g., when Z is an HCV antigen, the antigen is        inserted at a position that is not naturally occurring in HCV).

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated nucleic acidprovided by the formula:

WXZY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid) and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

-   -   with the proviso that Z is not in a position that is naturally        occurring in HCV (e.g., when Z is an HCV antigen, the antigen is        inserted at a position that is not naturally occurring in HCV).

Several other embodiments described herein concern recombinant HCVNS3/4A polypeptides, wherein the polypeptide comprises four domains(domain W, domain X, domain Y, and domain Z). Domain W can be an NS3protease domain as described herein, or fragment thereof, domain X canbe an NS3 helicase domain, or a fragment thereof, and domain Y can be anNS4A co-factor domain, or a fragment thereof. Domain Z can be anantigen, an epitope of a pathogen, a TCE, and/or the aforementionedmolecules with or without a linker and/or adjuvant sequence. Inpreferred embodiments, the recombinant HCV NS3/4A chimeric polypeptideretains catalytic activity (e.g., protease, helicase, or protease andhelicase activity) but may have altered activity or specificity. Inpreferred embodiments, domain Z is in a position within the recombinantchimeric polypeptide, which is non-naturally-occurring (e.g., when Zencodes an HCV antigen).

In some embodiments, the W domain comprises the polypeptide encodednucleic acid sequence of residues 1-551 of an NS3/4A sequence such asSEQ ID NOs: 1 or 35, or an analogous sequence encoded by any NS3/4Anucleic acid, or a fragment thereof (e.g., said fragment can comprise,consist of, or consist essentially of a polypeptide encoded by about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35). In someembodiments, the X domain can comprise the polypeptide encoded by thenucleic acid sequence of residues 218-1568 of SEQ ID NOs: 1 or 35, orencoded by an analogous sequence of any NS3/4A nucleic acid, or afragment thereof (e.g., said encoding fragment can comprise, consist of,or consist essentially of about at least, equal to, greater than, lessthan, or any number in between 9, 15, 30, 50, 75, 100, 125, 150, 175,200, 250, or 300 consecutive nucleotides of the helicase domain of SEQ.ID. Nos. 1 or 35). In some embodiments, the Y domain can comprise apolypeptide encoded by the nucleic acid sequence of residues 1569-2069of SEQ ID NOs: 1 or 35, or encoded by an analogous sequence of anyNS3/4A nucleic acid, or a fragment thereof (e.g., said fragment cancomprise, consist of, or consist essentially of a polypeptide encoded byabout at least, equal to, greater than, less than, or any number inbetween 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, or 350consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35). Inpreferred embodiments, the Z domain can comprise a polypeptide encodedby the nucleic acid sequence of an antigen, preferably a TCE, and morepreferably a sequence selected from the group consisting of SEQ ID NOs:221-571 and SEQ ID NOs:809-1011 and SEQ ID NO:1014, SEQ ID NOs:1016-1034, SEQ ID NOs: 1146-1173 and SEQ ID NOs: 1210-1328.

In some embodiments, the Z domain is located within or flanking (e.g.,juxtaposed or immediately adjacent to) said W domain. For example, thenucleic acid encoding the Z domain can place the encoded antigen betweenor next to amino acids 1 and 2, 2 and 3, 3 and 4, 4 and 5, 5 and 6, 6and 7, 7 and 8, 8 and 9, 9 and 10, 10 and 11, 11 and 12, 12 and 13, 13and 14, 14 and 15, 15 and 16, 16 and 17, 17 and 18, 18 and 19, 19 and20, 20 and 21, 21 and 22, 22 and 23, 23 and 24, 24 and 25, 25 and 26, 26and 27, 27 and 28, 28 and 29, 29 and 30, 30 and 31, 31 and 32, 32 and33, 33 and 34, 34 and 35, 35 and 36, 36 and 37, 37 and 38, 38 and 39, 39and 40, 40 and 41, 41 and 42, 42 and 43, 43 and 44, 44 and 45, 45 and46, 46 and 47, 47 and 48, 48 and 49, 49 and 50, 50 and 51, 51 and 52, 52and 53, 53 and 54, 54 and 55, 55 and 56, 56 and 57, 57 and 58, 58 and59, 59 and 60, 60 and 61, 61 and 62, 62 and 63, 63 and 64, 64 and 65, 65and 66, 66 and 67, 67 and 68, 68 and 69, 69 and 70, 70 and 71, 71 and72, 72 and 73, 73 and 74, 74 and 75, 75 and 76, 76 and 77, 77 and 78, 78and 79, 79 and 80, 80 and 81, 81 and 82, 82 and 83, 83 and 84, 84 and85, 85 and 86, 86 and 87, 87 and 88, 88 and 89, 89 and 90, 90 and 91, 91and 92, 92 and 93, 93 and 94, 94 and 95, 95 and 96, 96 and 97, 97 and98, 98 and 99, 99 and 100, 100 and 101, 101 and 102, 102 and 103, 103and 104, 104 and 105, 105 and 106, 106 and 107, 107 and 108, 108 and109, 109 and 110, 110 and 111, 111 and 112, 112 and 113, 113 and 114,114 and 115, 115 and 116, 116 and 117, 117 and 118, 118 and 119, 119 and120, 120 and 121, 121 and 122, 122 and 123, 123 and 124, 124 and 125,125 and 126, 126 and 127, 127 and 128, 128 and 129, 129 and 130, 130 and131, 131 and 132, 132 and 133, 133 and 134, 134 and 135, 135 and 136,136 and 137, 137 and 138, 138 and 139, 139 and 140, 140 and 141, 141 and142, 142 and 143, 143 and 144, 144 and 145, 145 and 146, 146 and 147,147 and 148, 148 and 149, 149 and 150, 150 and 151, 151 and 152, 152 and153, 153 and 154, 154 and 155, 155 and 156, 156 and 157, 157 and 158,158 and 159, 159 and 160, 160 and 161, 161 and 162, 162 and 163, 163 and164, 164 and 165, 165 and 166, 166 and 167, 167 and 168, 168 and 169,169 and 170, 170 and 171, 171 and 172, 172 and 173, 173 and 174, 174 and175, 175 and 176, 176 and 177, 177 and 178, 178 and 179, 179 and 180, or180 and 181 of said W domain of said chimeric polypeptide.

In some embodiments, the Z domain is located within or flanking (e.g.,juxtaposed or immediately adjacent to) the X domain. For example, the Zdomain can place the antigen between or next to amino acids 1 and 2, 2and 3, 3 and 4, 4 and 5, 5 and 6, 6 and 7, 7 and 8, 8 and 9, 9 and 10,10 and 11, 11 and 12, 12 and 13, 13 and 14, 14 and 15, 15 and 16, 16 and17, 17 and 18, 18 and 19, 19 and 20, 20 and 21, 21 and 22, 22 and 23, 23and 24, 24 and 25, 25 and 26, 26 and 27, 27 and 28, 28 and 29, 29 and30, 30 and 31, 31 and 32, 32 and 33, 33 and 34, 34 and 35, 35 and 36, 36and 37, 37 and 38, 38 and 39, 39 and 40, 40 and 41, 41 and 42, 42 and43, 43 and 44, 44 and 45, 45 and 46, 46 and 47, 47 and 48, 48 and 49, 49and 50, 50 and 51, 51 and 52, 52 and 53, 53 and 54, 54 and 55, 55 and56, 56 and 57, 57 and 58, 58 and 59, 59 and 60, 60 and 61, 61 and 62, 62and 63, 63 and 64, 64 and 65, 65 and 66, 66 and 67, 67 and 68, 68 and69, 69 and 70, 70 and 71, 71 and 72, 72 and 73, 73 and 74, 74 and 75, 75and 76, 76 and 77, 77 and 78, 78 and 79, 79 and 80, 80 and 81, 81 and82, 82 and 83, 83 and 84, 84 and 85, 85 and 86, 86 and 87, 87 and 88, 88and 89, 89 and 90, 90 and 91, 91 and 92, 92 and 93, 93 and 94, 94 and95, 95 and 96, 96 and 97, 97 and 98, 98 and 99, 99 and 100, 100 and 101,101 and 102, 102 and 103, 103 and 104, 104 and 105, 105 and 106, 106 and107, 107 and 108, 108 and 109, 109 and 110, 110 and 111, 111 and 112,112 and 113, 113 and 114, 114 and 115, 115 and 116, 116 and 117, 117 and118, 118 and 119, 119 and 120, 120 and 121, 121 and 122, 122 and 123,123 and 124, 124 and 125, 125 and 126, 126 and 127, 127 and 128, 128 and129, 129 and 130, 130 and 131, 131 and 132, 132 and 133, 133 and 134,134 and 135, 135 and 136, 136 and 137, 137 and 138, 138 and 139, 139 and140, 140 and 141, 141 and 142, 142 and 143, 143 and 144, 144 and 145,145 and 146, 146 and 147, 147 and 148, 148 and 149, 149 and 150, 150 and151, 151 and 152, 152 and 153, 153 and 154, 154 and 155, 155 and 156,156 and 157, 157 and 158, 158 and 159, 159 and 160, 160 and 161, 161 and162, 162 and 163, 163 and 164, 164 and 165, 165 and 166, 166 and 167,167 and 168, 168 and 169, 169 and 170, 170 and 171, 171 and 172, 172 and173, 173 and 174, 174 and 175, 175 and 176, 176 and 177, 177 and 178,178 and 179, 179 and 180, 180 and 181, 181 and 182, 182 and 183, 183 and184, 184 and 185, 185 and 186, 186 and 187, 187 and 188, 188 and 189,189 and 190, 190 and 191, 191 and 192, 192 and 193, 193 and 194, 194 and195, 195 and 196, 196 and 197, 197 and 198, 198 and 199, 199 and 200,200 and 201, 201 and 202, 202 and 203, 203 and 204, 204 and 205, 205 and206, 206 and 207, 207 and 208, 208 and 209, 209 and 210, 210 and 211,211 and 212, 212 and 213, 213 and 214, 214 and 215, 215 and 216, 216 and217, 217 and 218, 218 and 219, 219 and 220, 220 and 221, 221 and 222,222 and 223, 223 and 224, 224 and 225, 225, and 226, 226 and 227, 227and 228, 228 and 229, 229 and 230, 230 and 231, 231 and 232, 232 and233, 233 and 234, 234 and 235, 235 and 236, 236 and 237, 237 and 238,238 and 239, 239 and 240, 240 and 241, 241 and 242, 242 and 243, 243 and244, 244 and 245, 245 and 246, 246 and 247, 247 and 248, 248 and 249,249 and 250, 250 and 251, 251 and 252, 252 and 253, 253 and 254, 254 and255, 255 and 256, 256 and 257, 257 and 258, 258 and 259, 259 and 260,260 and 261, 261 and 262, 262 and 263, 263 and 264, 264 and 265, 265 and266, 266 and 267, 267 and 268, 268 and 269, 269 and 270, 270 and 271,271 and 272, 272 and 273, 273 and 274, 274 and 275, 275 and 276, 276 and277, 277 and 278, 278 and 279, 279 and 280, 280 and 281, 281 and 282,282 and 283, 283 and 284, 284 and 285, 285 and 286, 286 and 287, 287 and288, 288 and 289, 289 and 290, 290 and 291, 291 and 292, 292 and 293,293 and 294, 294 and 295, 295 and 296, 296 and 297, 297 and 298, 298 and299, 299 and 300, 300 and 201, 301 and 302, 302 and 303, 303 and 304,304 and 305, 305 and 306, 306 and 307, 307 and 308, 308 and 309, 309 and310, 310 and 311, 311 and 312, 312 and 313, 313 and 314, 314 and 315,315 and 316, 316 and 317, 317 and 318, 318 and 319, 319 and 320, 320 and321, 321, and 322, 322 and 323, 323 and 324, 324 and 325, 325, and 326,326 and 327, 327 and 328, 328 and 329, 329 and 330, 330 and 331, 331 and332, 332 and 333, 333 and 334, 334 and 335, 335 and 336, 336 and 337,337 and 338, 338 and 339, 339 and 340, 340 and 341, 341 and 342, 342 and343, 343 and 344, 344 and 345, 345 and 346, 346 and 347, 347 and 348,348 and 349, 349 and 350, 350 and 351, 351 and 352, 352 and 353, 353 and354, 354 and 355, 355 and 356, 356 and 357, 357 and 358, 358 and 359,359 and 360, 360 and 361, 361 and 362, 362 and 363, 363 and 364, 364 and365, 365 and 366, 366 and 367, 367 and 368, 368 and 369, 369 and 370,370 and 371, 371 and 372, 372 and 373, 373 and 374, 374 and 375, 375 and376, 376 and 377, 377 and 378, 378 and 379, 379 and 380, 380 and 381,381 and 382, 382 and 383, 383 and 384, 384 and 385, 385 and 386, 386 and387, 387 and 388, 388 and 389, 389 and 390, 390 and 391, 391 and 392,392 and 393, 393 and 394, 394 and 395, 395 and 396, 396 and 397, 397 and398, 398 and 399, 399 and 400, 401 and 402, 402 and 403, 403 and 404,404 and 405, 405 and 406, 406 and 407, 407 and 408, 408 and 409, 409 and410, 410 and 411, 411 and 412, 412 and 413, 413 and 414, 414 and 415,415 and 416, 416 and 417, 417 and 418, 418 and 419, 419 and 420, 420 and421, 421 and 422, 422 and 423, 423 and 424, 424 and 425, 425 and 426,426 and 427, 427 and 428, 428 and 429, 429 and 430, 430 and 431, 431 and432, 432 and 433, 433 and 434, 434 and 435, 435 and 436, 436 and 437,437 and 438, 438 and 439, 439 and 440, 440 and 441, 441 and 442, 442 and443, 443 and 444, 444 and 445, 445 and 446, 446 and 447, 447 and 448,448 and 449, or 449 and 450 of the X domain of the chimeric polypeptide.Preferably, the Z domain is located between amino acids 383 and 450 ofsaid X domain.

Optionally, the Z domain is located within or flanking (e.g., juxtaposedor immediately adjacent to) said Y domain. For example, the Z domain canplace the antigen between or next to amino acids 1 and 2, 2 and 3, 3 and4, 4 and 5, 5 and 6, 6 and 7, 7 and 8, 8 and 9, 9 and 10, 10 and 11, 11and 12, 12 and 13, 13 and 14, 14 and 15, 15 and 16, 16 and 17, 17 and18, 18 and 19, 19 and 20, 20 and 21, 21 and 22, 22 and 23, 23 and 24, 24and 25, and 26, 26 and 27, 27 and 28, 28 and 29, 29 and 30, 30 and 31,31 and 32, 32 and 33, 33 and 34, 34 and 35, 35 and 36, 36 and 37, 37 and38, 38 and 39, 39 and 40, 40 and 41, 41 and 42, 42 and 43, 43 and 44, 44and 45, 45 and 46, 46 and 47, 47 and 48, 48 and 49, 49 and 50, 50 and51, 51 and 52, 52 and 53, or 53 and 54 of the Y domain of the chimericpolypeptide.

That is, aspects of the invention concern a composition that comprises,consists of, or consists essentially of an isolated polypeptide providedby the formula:

WXYZ

wherein:

W represents a protease domain (e.g., an HCV NS3 protease domainprepared as described herein, such as a mutant with enhanced or alteredprotease activity or substrate specificity) or a fragment thereof,wherein said fragment comprises, consists of, or consists essentially ofabout at least, equal to, greater than, less than, or any number inbetween 9, 15, 30, 50, 75, 100, 125, 150, or 175 consecutive amino acidsof the protease domain of SEQ. ID. Nos. 2 or 36 (e.g., residues 1-181 ofSEQ ID NO:36, or an analogous position in any NS3/4A polypeptide);

X represents a helicase domain (e.g., an HCV helicase domain) or afragment thereof, wherein said fragment comprises, consists of, orconsists essentially of about at least, equal to, greater than, lessthan, or any number in between 9, 15, 30, 50, 75, 100, 125, 150, 175,200, 250, or 300 consecutive amino acids of the helicase domain of SEQ.ID. Nos. 2 or 36 (e.g., residues 70-596 of SEQ ID NO:36, or an analogousposition in any NS3/4A polypeptide);

Y represents an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive amino acids of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 597-686 of SEQ ID NO:36), or an analogous position inany NS3/4A polypeptide); and

Z represents an antigen (e.g., an antigen of a virus, bacteria, toxin,or cancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

-   -   with the proviso that Z is not in a position that is naturally        occurring in HCV (e.g., when Z is an HCV antigen, the antigen is        inserted at a position that is not naturally occurring in HCV).    -   Aspects of the invention also concern a composition that        comprises, consists of, or consists essentially of an isolated        polypeptide encoded by a nucleic acid provided by the formula:

ZWXY

wherein:

W represents a protease domain (e.g., an HCV NS3 protease domainprepared as described herein, such as a mutant with enhanced or alteredprotease activity or substrate specificity) or a fragment thereof,wherein said fragment comprises, consists of, or consists essentially ofabout at least, equal to, greater than, less than, or any number inbetween 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300consecutive nucleotides of the protease domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1-551 of SEQ ID NO:35, or an analogous position in anyNS3/4A nucleic acid);

X represents a helicase domain (e.g., an HCV helicase domain) or afragment thereof, wherein said fragment comprises, consists of, orconsists essentially of a polypeptide encoded by about at least, equalto, greater than, less than, or any number in between 9, 15, 30, 50, 75,100, 125, 150, 175, 200, 250, or 300 consecutive nucleotides of thehelicase domain of SEQ. ID. Nos. 1 or 35 (e.g., residues 218-1568 of SEQID NO:35, or an analogous position in any NS3/4A nucleic acid);

Y represents an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of a polypeptide encoded by about at least, equal to,greater than, less than, or any number in between 9, 15, 30, 50, 75,100, 125, 150, 175, 200, 250, or 300 consecutive nucleotides of the NS4Adomain of SEQ. ID. Nos. 1 or 35 (e.g., residues 1569-2069 of SEQ IDNO:35, or an analogous position in any NS3/4A nucleic acid); and

Z represents an antigen (e.g., an antigen of a virus, bacteria, toxin,or cancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID Nos: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

with the proviso that Z is not in a position that is naturally occurringin HCV (e.g., when Z is an HCV antigen, the antigen is inserted at aposition that is not naturally occurring in HCV)

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated polypeptide encodedby a nucleic acid provided by the formula:

WZXY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid); and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

with the proviso that Z is not in a position that is naturally occurringin HCV (e.g., when Z is an HCV antigen, the antigen is inserted at aposition that is not naturally occurring in HCV).

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated polypeptide encodedby a nucleic acid provided by the formula:

WZXY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid); and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173, and SEQ ID NOs:1210-1328),

with the proviso that Z is not in a position that is naturally occurringin HCV (e.g., when Z is an HCV antigen, the antigen is inserted at aposition that is not naturally occurring in HCV).

Aspects of the invention also concern a composition that comprises,consists of, or consists essentially of an isolated polypeptide encodedby a nucleic acid provided by the formula:

WXZY

wherein:

W encodes a protease domain (e.g., an HCV NS3 protease domain preparedas described herein, such as a mutant with enhanced or altered proteaseactivity or substrate specificity) or a fragment thereof, wherein saidfragment comprises, consists of, or consists essentially of about atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or 300 consecutivenucleotides of the protease domain of SEQ. ID. Nos. 1 or 35 (e.g.,residues 1-551 of SEQ ID NO:35, or an analogous position in any NS3/4Anucleic acid);

X encodes a helicase domain (e.g., an HCV helicase domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the helicase domain of SEQ. ID. Nos. 1 or35 (e.g., residues 218-1568 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid);

Y encodes an enhancer domain (e.g., an HCV NS4A domain) or a fragmentthereof, wherein said fragment comprises, consists of, or consistsessentially of about at least, equal to, greater than, less than, or anynumber in between 9, 15, 30, 50, 75, 100, 125, 150, 175, 200, 250, or300 consecutive nucleotides of the NS4A domain of SEQ. ID. Nos. 1 or 35(e.g., residues 1569-2069 of SEQ ID NO:35, or an analogous position inany NS3/4A nucleic acid) and

Z encodes an antigen (e.g., an antigen of a virus, bacteria, toxin, orcancer cell, such as a TCE provided by a sequence selected from thegroup consisting of SEQ ID NOs: 221-571, SEQ ID NOs:809-1011, SEQ IDNO:1014, SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ ID NOs:1210-1328),

with the proviso that Z is not in a position that is naturally occurringin HCV (e.g., when Z is an HCV antigen, the antigen is inserted at aposition that is not naturally occurring in HCV).

Methods of making and using the compositions described herein are alsoprovided. In addition to methods of making the embodied nucleic acidsand polypeptides, other embodiments include method of making immunogensand/or vaccine compositions. Preferably immunogenic compositions orvaccine compositions comprise a pharmaceutically acceptable carrier inaddition to the nucleic acids and/or polypeptides described herein. Somemethods are practiced, for example, by mixing an adjuvant with a nucleicacid or polypeptide as described above, so as to formulate a singlecomposition (e.g., an immunogenic composition or a vaccine). Preferredmethods involve the mixing of ribavirin with the nucleic acids orencoded polypeptides described herein. (See e.g., U.S. Pat. No.6,680,059, and U.S. Pat. No. 6,858,590, hereby expressly incorporated byreference in their entirety.)

Preferred methods of using the compositions described herein involveproviding an animal (e.g., a mammal such as a human or a domesticanimal) in need of an immune response to an antigen with a sufficientamount of one or more of the nucleic acid and/or polypeptidecompositions described herein, wherein the TCE or antigen present in thecomposition is derived from said antigen/target (e.g., an antigenpresent on a pathogen, such as a virus like hepatitis, HIV, or the flu).In some embodiments, the animal, preferably a mammal, collectivelyreferred to as a subject, is identified as a subject in need of animmune response to an antigen or a pathogen comprising an antigen, andsaid identified subject is provided a therapeutically effective amountof one or more of the NS3/4A platforms comprising said antigen.Optionally, the immune response of said identified subject to saidplatform comprising said antigen is measured.

In still more embodiments, a gene gun or electroporation device (e.g.,Medpulsar™) is used to introduce the nucleic acids described herein to amammalian subject in need of an immune response to an agent, wherein thenucleic acids encode a TCE specific to the agent. In some embodiments,an amount of an adjuvant, such as ribavirin, is mixed with the nucleicacid immunogen prior to delivery. In other embodiments, the nucleic acidimmunogen is provided shortly before or after administration ofribavirin or at the same site of nucleic acid inoculation. Otherembodiments relate to an isolated nucleic acid comprising a nucleic acidsequence encoding a TCE, wherein said nucleic acid sequence encodingsaid TCE is inserted within a nucleic acid sequence comprising,consisting essentially of, or consisting of one of the following SEQ IDNOs: 1, 35, or 573-806, and wherein said isolated nucleic acid operablyencodes a polypeptide that retains catalytic activity. These embodimentscan be delivered using electroporation methods, as described above, withor without an adjuvant, such as ribavirin.

SEQ ID NOs: 1174-1198 correspond to nucleic acid and peptide constructsof fragments of the HBcAg with or without NS3 protease cleavage sitesjoined to the NS3/4A platform. SEQ ID NOs: 1174-1198 initiallycorrespond to all parts of possible constructs presented therein,including the amino acid sequence for HBcAg, the NS3/4A proteasecleavage site, the NS4A/B protease cleavage site, and the NS3/4Aplatform.

SEQ ID NOs: 1181-1182 correspond to a functional NS3 protease joined toNS4A via a mutant NS3/4A protease cleavage site. The NS3/4A platform isjoined to the HBcAg without any NS3 protease cleavage sites. SEQ ID NOs:1181-1182, corresponding to FIG. 1A, will have an active protease (NS3)that is unable to cleave itself.

SEQ ID NOs: 1183-1184 correspond to a mutant non-functional NS3 proteasejoined to NS4A via an NS3/4A protease cleavage site. The NS3/4A platformis joined to the HBcAg without any NS3 protease cleavage sites. SEQ IDNOs: 1183-1184, corresponding to FIG. 1B, will have an inactive protease(NS3) that is unable to cleave itself through the functional proteasecleavage site.

SEQ ID NOs: 1185-1186 correspond to a functional NS3 protease joined toNS4A via an NS3/4A protease cleavage site. The NS3/4A platform is joinedto the HBcAg without any NS3 protease cleavage sites. SEQ ID NOs:1185-1186, corresponding to FIG. 1C, will have an active protease (NS3)that is able to cleave itself but will not cleave any other portion ofthe peptide as there are no other protease cleavage sites available.Accordingly, the products created by NS3 cleavage include the NS3protein and the NS4A joined to the HBcAg.

SEQ ID NOs: 1187-1188 correspond to a functional NS3 protease joined toNS4A via an NS3/4A protease cleavage site. The NS3/4A platform is joinedto the HBcAg via an NS4A/B protease cleavage site. SEQ ID NOs:1187-1188, corresponding to FIG. 1D, will have an active protease (NS3)that is able to cleave itself and cleave the NS4A from the HBcAg via theNS4A/B protease cleavage site. Accordingly, the products created by NS3cleavage include the NS3 protein, the NS4A protein, and the HBcAgpeptide.

SEQ ID NOs: 1189-1190 correspond to a functional NS3 protease joined toNS4A via an NS3/4A protease cleavage site. The NS3/4A platform is joinedto the HBcAg via an NS4A/B protease cleavage site. The HBcAg containsNS3/4A protease cleavage sites within the peptide, particularly betweenamino acids 44 and 45, between amino acids 87 and 88, as well as betweenamino acids 141 and 142. SEQ ID NOs: 1189-1190, corresponding to FIG.1E, will have an active protease (NS3) that is able to cleave itself andcleave the NS4A from the HBcAg via the NS4A/B protease cleavage site.Additionally, the NS3 protease will cleave the HBcAg between amino acids44 and 45, between amino acids 87 and 88, as well as between amino acids141 and 142 via the NS3/4A protease cleavage site. Accordingly, theproducts created by NS3 cleavage include the NS3 protein, the NS4Aprotein, and the fragments of the HBcAg peptide corresponding to aminoacids 1-44, amino acids 45-87, amino acids 88-141, and amino acids142-183.

SEQ ID NOs: 1191-1198 correspond to a functional NS3 protease joined toNS4A via an NS3/4A protease cleavage site. The NS3/4A platform is joinedto the HBcAg via an NS4A/B protease cleavage site. The HBcAg is shuffledwith NS3/4A protease cleavage sites separating the shuffled fragments.SEQ ID NOs: 1191-1198, corresponding to FIGS. 1F-1I, will have an activeprotease (NS3) that is able to cleave itself and cleave the NS4A fromthe HBcAg via the NS4A/B protease cleavage site. Additionally, the NS3protease will cleave the HBcAg shuffled fragments at the site of theNS3/4A protease cleavage site. Accordingly, the products created by NS3cleavage include the NS3 protein, the NS4A protein, and the fragments ofthe HBcAg peptide.

SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ ID NOs: 1210-1328correspond to antigenic peptide sequences from allergens and infectiousdiseases. The peptides represented can be used as part of an immunogeniccomposition designed to raise an immune response against the antigenfrom which they originate. In another embodiment, the nucleic acidscoding for the antigenic peptide sequence can be used as part of DNAvaccine designed to raise an immune response against the antigen fromwhich they originate after administration.

SEQ ID NOs: 1122-1145 correspond to antigenic peptide sequencescontaining the NS3/4A protease cleavage site inserted at various siteswithin the peptide sequence. Although the SEQ ID NOs: 1122-1145 reciteonly the NS3/4A protease cleavage site, any NS3 protease cleavage site(e.g., NS4A/B protease cleavage site) can be used. The protease cleavagesites are cleaved by an NS3 peptide, which can be administered inpeptide or nucleic acid form pre-administration, post-administration, orperi-administration of the antigenic sequence containing the NS3protease cleavage site(s). The protease cleavage sites improve antigenprocessing within antigen presenting cells and facilitate a heightenedcell-mediated immune response. Although the antigenic sequences of SEQID NOs: 1122-1145 contain naturally-ordered antigen fragments separatedby an NS3 protease cleavage site, the antigenic fragments can be orderedrandomly as in the shuffled fragments of HBcAg separated by NS3 proteasecleavage sites seen in SEQ ID NOs: 1174-1198.

SEQ ID NOs: 1098-1121 correspond to the codon-optimized (human) nucleicacid sequence encoding antigenic peptide sequences containing the NS3/4Aprotease cleavage site inserted at various sites within the peptidesequence. Although SEQ ID NOs: 1098-1121 encode only the NS3/4A proteasecleavage site, any NS3 protease cleavage site (e.g., NS4A/B, NS4B/5A,and NS5A/5B protease cleavage sites) can be used. The protease cleavagesites are cleaved by an NS3 peptide, which can be administered as apeptide or nucleic acid pre-administration, post-administration, orperi-administration of the codon optimized nucleic acid coding theantigenic sequence containing the NS3 protease cleavage site(s). Theprotease cleavage sites improve antigen processing within antigenpresenting cells and facilitate a heightened cell-mediated immuneresponse. Although the codon optimized nucleic acids corresponding toSEQ ID NOs: 1098-1121 encode antigenic sequences containingnaturally-ordered antigen fragments separated by an NS3 proteasecleavage site, the antigenic fragments can be ordered randomly as in theshuffled fragments of HBcAg separated by NS3 protease cleavage sitesseen in SEQ ID NOs: 1174-1198.

SEQ ID NOs: 1059-1097 correspond to the NS3/4A peptide linked toantigenic peptide sequences containing NS3/4A protease cleavage siteinserted at various sites within the peptide sequence. Although SEQ IDNOs: 1059-1097 encode only the NS3/4A protease cleavage site, any NS3protease cleavage site (e.g., NS4A/B, NS4B/5A, and NS5A/5B proteasecleavage sites) can be used. The protease cleavage sites improve antigenprocessing within antigen presenting cells and facilitate a heightenedcell-mediated immune response. Although the antigenic sequences of SEQID NOs: 1059-1097 contain naturally-ordered antigen fragments separatedby an NS3 protease cleavage site, the antigenic fragments can be orderedrandomly as in the shuffled fragments of HBcAg separated by NS3 proteasecleavage sites seen in SEQ ID NOs: 1174-1198.

SEQ ID NOs: 1035-1058 correspond to the codon-optimized (human) nucleicacid sequence encoding NS3/4A peptide linked to antigenic peptidesequences containing the NS3/4A protease cleavage site inserted atvarious sites within the peptide sequence. Although SEQ ID NOs:1035-1058 encode only the NS3/4A protease cleavage site, any NS3protease cleavage site (e.g., NS4A/B, NS4B/5A, and NS5A/5B proteasecleavage sites) can be used. The protease cleavage sites improve antigenprocessing within antigen presenting cells and facilitate a heightenedcell-mediated immune response. Although the codon optimized nucleicacids presented in SEQ ID NOs: 1035-1058 encode antigenic sequencescontaining naturally-ordered antigen fragments separated by an NS3protease cleavage site, the antigenic fragments can be ordered randomlyas in the shuffled fragments of HBcAg separated by NS3 protease cleavagesites seen in SEQ ID NOs: 1174-1198.

SEQ ID NO: 1175 corresponds to the wild type sequence of HBcAg and SEQID NO: 1176 corresponds to the codon optimized sequence of HBcAg. SEQ IDNOs: 1199-1209 correspond to mutant NS3/4A peptides having alteredsubstrate specificity.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-1I depict various constructs containing the NS3/4A platform andthe HBcAg containing NS3 protease cleavage sites.

FIG. 2 is a graph showing the antibody titer in H-2^(d) mice against NS3as a function of time after the first intra muscular immunization.Diamonds denote antibody titer in mice immunized with NS3/4A-pVAX andsquares denote antibody titer in mice immunized with NS3-pVAX.

FIGS. 3A and 3B show the mean NS3-specific antibody responses primed bygene gun immunisations with 4 μg wtNS3/4A-pVAX1 and coNS3/4A-pVAX1, ors.c. injection of 10⁷ wtNS3/4A-SFV particles in groups of ten H-2^(d)mice (FIG. 3A). All mice were immunized at weeks zero and four. Valuesare given as mean end-point antibody titres (±SD.). Also shown FIG. 3Bare the IgG subclass patterns from groups of five mice immunized twicewith wtNS3/4A-pVAX1 given i.m., coNS3/4A-pVAX1 given i.m. or by gene gun(gg), and wtNS3/4A-SFV given s.c. Values are given as mean end-pointantibody titres (±SD.). A “**” sign indicates a statistical differenceof p<0.01, a “*” sign indicates a difference of p<0.05, and NS (notsignificant) indicates no statistical difference (Mann-Whitney). Alsogiven is the titer ratio obtained by dividing the mean endpoint titre ofIgG2a antibodies to NS3 by the mean endpoint titre IgG1 antibodies toNS3. A high ratio (>3) indicates a Th1-like response and a low ratio(<0.3) indicates a Th2-like response, whereas values within a three-folddifference from 1 (0.3 to 3) indicates a mixed Th1/Th2 response.

FIG. 4A shows the in vivo protection conferred by one gene gunimmunization of NS3/4A-pVAX1 (4 μg) or MSLF1-pVAX1 (4 μg). Mice wereimmunized with the respective plasmid and 14 days later the mice werechallenged with an NS3/4A expressing SP2/0 cell line (approximately 10⁶cells/mouse). Tumor size was then measured through the skin dailyfollowing day 6 post-challenge and the data plotted. FIG. 4B shows thein vivo protection conferred by two gene gun immunizations ofNS3/4A-pVAX1 (4 μg) or MSLF1-pVAX1 (4 μg). Mice were immunized with therespective plasmid at weeks zero and week four and, 14 days after thelast immunization, the mice were challenged with an NS3/4A expressingSP2/0 cell line (approximately 10⁶ cells/mouse). Tumor size was thenmeasured through the skin daily following day 6 post-challenge and thedata plotted.

FIG. 5 shows the in vivo protection conferred by three gene gunimmunizations of NS3/4A-pVAX1 (4 μg) or MSLF1-pVAX1 (4 μg). Mice wereimmunized with the respective plasmid at weeks zero, week four, and weekeight and, 14 days after the last immunization, the mice were challengedwith an NS3/4A expressing SP2/0 cell line (approximately 10⁶cells/mouse). Tumor size was then measured through the skin dailyfollowing day 6 post-challenge and the data plotted.

FIG. 6A is a graph showing the percentage of specific CTL-mediated lysisof SP2/0 target cells as a function of the effector to target ratio.Phosphate Buffered Saline (PBS) was used as a control immunogen.

FIG. 6B is a graph showing the percentage specific CTL-mediated lysis ofSP2/0 target cells as a function of the effector to target ratio.Plasmid NS3/4A-pVAX was used as the immunogen.

FIG. 7A is a graph showing the response of naive splenic T cells thatwere stimulated with peptide coated RMA-S cells. The naive splenic Tcells were obtained from C57/BL6 mice.

FIG. 7B is a graph showing the response of splenic T cells that wererestimulated with peptide coated RMA-S cells. The splenic T cells wereobtained from C57/BL6 mice that were provided a single 4 μg dose ofMSLF1-pVAX1.

FIG. 7C is a graph showing the response of splenic T cells that wererestimulated with peptide coated RMA-S cells. The splenic T cells wereobtained from C57/BL6 mice that were provided a single 4 μg dose ofNS3/4A-pVAX1.

FIG. 7D is a graph showing the response of naive splenic T cells thatwere stimulated with peptide coated RMA-S cells. The naive splenic Tcells were obtained from C57/BL6 mice.

FIG. 7E is a graph showing the response of splenic T cells that wererestimulated with peptide coated RMA-S cells. The splenic T cells wereobtained from C57/BL6 mice that were provided two 4 μg doses ofMSLF1-pVAX1.

FIG. 7F is a graph showing the response of splenic T cells that wererestimulated with peptide coated RMA-S cells. The splenic T cells wereobtained from C57/BL6 mice that were provided two 4 μg doses ofNS3/4A-pVAX1.

FIG. 7G is a graph showing the response of naive splenic T cells thatwere stimulated with NS3/4A expressing EL-4 cells. The naive splenic Tcells were obtained from C57/BL6 mice.

FIG. 7H is a graph showing the response of splenic T cells that wererestimulated with NS3/4A expressing EL-4 cells. The splenic T cells wereobtained from C57/BL6 mice that were provided a single 4 μg dose ofMSLF1-pVAX1.

FIG. 7I is a graph showing the response of splenic T cells that wererestimulated with NS3/4A expressing EL-4 cells. The splenic T cells wereobtained from C57/BL6 mice that were provided a single 4 μg dose ofNS3/4A-pVAX1.

FIG. 7J is a graph showing the response of naive splenic T cells thatwere stimulated with NS3/4A expressing EL-4 cells. The naive splenic Tcells were obtained from C57/BL6 mice.

FIG. 7K is a graph showing the response of splenic T cells that wererestimulated with NS3/4A expressing EL-4 cells. The splenic T cells wereobtained from C57/BL6 mice that were provided two 4 μg doses ofMSLF1-pVAX1.

FIG. 7L is a graph showing the response of splenic T cells that wererestimulated with NS3/4A expressing EL-4 cells. The splenic T cells wereobtained from C57/BL6 mice that were provided two 4 μg doses ofNS3/4A-pVAX1.

FIG. 8A shows a flow cytometric quantification of the precursorfrequency of NS3/4A-specific CD8+ T cells using peptide-loadedH-2D^(b):Ig fusion protein. In a) the mean % NS3-specific CD8+ T cellsfrom groups of five mice immunized twice with wtNS3-pVAX1,wtNS3/4A-pVAX1, or coNS3/4A-pVAX1 using gene gun is shown. A “*” signindicates a difference of p<0.05, and NS (not significant) indicates nostatistical difference (Mann-Whitney). FIG. 8B, also shown, representsthe raw data from representative individual mice from the groups listedabove (e, f, and h), as well as from individual mice immunized once withcoNS3/4A-pVAX1 (b) or wtNS3/4A-SFV (c). In (d) and (g), non-immunizedcontrol mice from the different experiments have been given. In (i) and(j) the splenocytes were restimulated for five days with theNS3-peptides prior to analysis. A total of 150,000-200,000 data pointswere collected and the percentage of CD8+ cells stained for H-2D^(b):Igare indicated in the parentheses in each dot-plot.

FIGS. 9A and 9B show the priming of in vitro detectable CTLs in H-2^(b)mice by gene gun immunization of the wtNS3-pVAX1, wtNS3/4A, and coNS3/4Aplasmids, or s.c. injection of wtNS3/4A-SFV particles. Groups of five to10 H-2^(b) mice were immunized once (FIG. 9A) or twice (FIG. 9B). Thepercent specific lysis corresponds to the percent lysis obtained witheither NS3-peptide coated RMA-S cells (upper panel in (FIG. 9A) and(FIG. 9B) or NS3/4A-expressing EL-4 cells (lower panel in a and b) minusthe percent lysis obtained with unloaded or non-transfected EL-4 cells.Values have been given for effector to target (E:T) cell ratios of 60:1,20:1 and 7:1. Each line indicates an individual mouse.

FIG. 10A shows the specificity of tumor inhibiting immune responsesprimed by gene gun immunization. Groups of ten C57BL/6 mice were eitherleft untreated or were given two monthly immunizations with 4 μg ofcoNS3/4A-pVAX1. Two weeks after last immunization, mice were injectedsubcutaneously with the parental EL-4 cell line or 10⁶ NS3/4A-expressingEL-4 cells. Tumor sizes were measured through the skin at days 6, 7, 10,11, 12, and 14 after tumour injection. In FIG. 10B the in vivofunctional effector cell population was determined in groups of 10C57BL/6 mice immunized twice with the coNS3/4A-pVAX1 plasmid using genegun. In two groups either CD4+ or CD8+ T cells were depleted byadministration of monoclonal antibodies one week prior to, and during,challenge with the NS3/4A-expressing EL-4 cell line. Tumor sizes weremeasured through the skin at days 5, 6, 8, 11, 13, 14, and 15 aftertumour injection. Values have been given as the mean tumor size ±standard error. A “**” sign indicates a statistical difference ofp<0.01, a “*” sign indicates a difference of p<0.05, and NS (notsignificant) indicates no statistical difference (area under the curvevalues compared by ANOVA).

FIG. 11 shows an evaluation of the ability of different immunogens toprime HCV NS3/4A-specific tumor-inhibiting responses after a singleimmunization. Groups of ten C57BL/6 mice were either left untreated orwere given one immunization with the indicated immunogen (4 μg DNA usinggene gun in (a), (b), (c), (g), and (h); 10⁷ SFV particles s.c. in d;100 μg peptide in CFA s.c. in (e); and 20 μg rNS3 in CFA s.c. in (f).Two weeks after last immunization, mice were injected subcutaneouslywith 10⁶ NS3/4A-expressing EL-4 cells. Tumor sizes were measured throughthe skin at days 6 to 19 after tumor injection. Values have been givenas the mean tumor size ± standard error. In (a) to (e), as a negativecontrol the mean data from the group immunized with the empty pVAXplasmid by gene gun has been plotted in each graph. In (f) to (h) thenegative controls were non-immunized mice. Also given is the p valueobtained from the statistical comparison of the control with each curveusing the area under the curve and ANOVA.

FIGS. 12A, 12B, and 12C show the comparative efficiency of gene gundelivered wtNS3/4A-pVAX1 and coNS3/4A-pVAX1 plasmids in priming tumorinhibiting immune responses. Groups of ten BALB/c mice were either leftuntreated or were given one (FIG. 12A), two (FIG. 12B) or three (FIG.12C) monthly immunisations with 4 μg of plasmid. Two weeks after lastimmunization, mice were injected subcutaneously with 10⁶NS3/4A-expressing SP2/0 cells. Tumor sizes were measured through theskin at days 6, 8, 10, 11, 12, 13, and 14 after tumor injection. Valueshave been given as the mean tumor size ± standard error. A “**” signindicates a statistical difference of p<0.01, a “*” sign indicates adifference of p<0.05, and NS (not significant) indicates no statisticaldifference (area under the curve values compared by ANOVA).

FIG. 13 shows the effect of therapeutic vaccination with the coNS3/4Aplasmid using the gene gun. Groups of ten C57BL/6 mice were inoculatedwith 10⁶ NS3/4A-EL4 cells. One group had been immunized once with 4 μgcoNS3/4A DNA using a gene gun two weeks prior to challenge (positivecontrol), one group was immunized the same way six days after tumorinoculation, and one group was immunized 12 days after tumorinoculation. One group was not immunized (negative control). Tumor sizeswere measured through the skin at days 6, 10, 11, 12, 13, 14, 18, 19,and 20 after tumour injection. Values have been given as the mean tumorsize ± standard error. A “**” sign indicates a statistical difference ofp<0.01, a “*” sign indicates a difference of p<0.05, and NS (notsignificant) indicates no statistical difference (area under the curvevalues compared by ANOVA).

FIG. 14 is a graph showing the humoral response to 10 and 100 μgrecombinant Hepatitis C virus (HCV) non structural 3 protein (NS3), asdetermined by mean end point titres, when a single dose of 1 mg ofribavirin was co-administered.

FIG. 15 is a graph showing the humoral response to 20 μg recombinantHepatitis C virus (HCV) non structural 3 protein (NS3), as determined bymean end point titres, when a single dose of 0.1, 1.0, or 10 mg ofribavirin was co-administered.

FIG. 16 is a graph showing the effects of a single dose of 1 mgribavirin on NS3-specific lymph node proliferative responses, asdetermined by in vitro recall responses.

FIG. 17 shows the location of amino acid residues in the NS3A proteasethat affect protease cleavage. Versions of NS3/NS4A-pVAX wereconstructed to encode proteins in which each amino acid of the shownsequence other than the alanine residues was substituted with an alanineresidue. Each alanine residue was substituted with a glycine residue.The encoded proteins were analyzed for protease activity. The red colorindicates the 16 mutations which resulted in a protein that lacked allprotease activity. The dark blue color indicates the 3 mutations whichresulted in a protein that exhibited greatly enhanced protease activitycompared to wtNS3/NS4A.

FIG. 18 depicts the protease activity of the NS3 protease domain inwhich alanine or glycine was substituted for each protease-domainresidue. Each mutant was tested for protease activity after translation.The upper band corresponds to the noncleaved NS3/4A fusion protein andthe lower band corresponds to the free NS3 protein. A single or clearlydominant peak indicates destroyed or enhanced protease activity,compared with the dual peak appearance of the wt NS3/4A gene.

FIGS. 19A and B depict SDS Page gels where IPS-1 cleavage by particularmutants are visualized.

FIG. 20A is a graph showing the response of splenic T cells that wererestimulated with peptide coated RMA-S cells. The splenic T cells wereobtained from C57/BL6 mice that were provided a single 100 μg dose ofHBcAg-pVAX1 intramuscularly at week 0 and week 4, as indicated.

FIG. 20B is a graph showing the response of splenic T cells that wererestimulated with peptide coated RMA-S cells. The splenic T cells wereobtained from C57/BL6 mice that were provided a single 4 μg dose ofHBcAg-pVAX1 with a gene gun at week 0 and week 4, as indicated.

FIG. 21 shows the location of amino acid residues in the HCV NS3protease that affect protease cleavage. Versions of NS3/4A-pVAX wereconstructed to encode proteins in which each amino acid of the shownsequence other than the alanine residues was substituted with an alanineresidue. Each alanine residue was substituted with a glycine residue.The encoded polypeptides were analyzed for protease activity. The redcolor indicates the 16 mutations which resulted in a protein that lackedall protease activity. The dark blue color indicates the 3 mutationswhich resulted in a protein that exhibited greatly enhanced proteaseactivity compared to wtNS3/4A.

FIG. 22 shows the production of IFN-γ by splenocytes of mice immunizedwith various DNA and peptide antigens when primed with various antigen.

FIG. 23 shows the level of IgE production by mice immunized with eitherrecombinant birch or a DNA construct containing a birch-NS3/4A fusiongene.

FIGS. 24-1 and 2 shows the lysis of peptide loaded RMA-S cells.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT

Several of the embodiments described herein concern compositions andmethods that are useful for generating, enhancing, or improving animmune response to an epitope of a target antigen. Disclosed herein arecompositions relating to genetic constructs that include sequences fromthe Hepatitis C virus (HCV) and sequences encoding T-cell epitopes(TCEs), and methods of generating or enhancing an immune response usingthe genetic constructs and polypeptides encoded by the geneticconstructs. Several embodiments disclosed herein provide nucleic acidsthat encode chimeric HCV NS3/4A polypeptides or fragments thereof of atleast 3 amino acids in length. For example, the NS3/4A sequence or afragment thereof can comprise at least, equal to, greater than, or lessthan, or any number in between 3, 5, 10, 20, 50, 100, 150, 200, 250,300, 350, 400, 500, 700, 1000, 1200, or 1500 consecutive amino acids ofa natural or synthetic NS3/4A polypeptide (e.g., a naturally occurringisotype or a codon-optimized or otherwise modified NS3/4A polypeptide).Exemplary NS3/4a sequences are disclosed in U.S. Pat. No. 6,960,569,hereby expressly incorporated by reference in its entirety. Exemplarycodon-optimized sequences are disclosed in U.S. Patent ApplicationPublication No. 2003/0206919, hereby expressly incorporated by referencein its entirety, and in SEQ ID NOs: 35 and 36. That is, the nucleic acidencoding the NS3/4A sequence or a fragment thereof can comprise atleast, equal to, greater than, less than, or any number in between 9,15, 30, 50, 75, 100, 125, 150, 175, 200, 250, 300, 400, 500, 600, 700,800, 900, 1000, 1200, 1500, or 2000 consecutive nucleotides of a nucleicacid sequence that encodes a natural or synthetic NS3/4A polypeptide.Many of these embodiments also include a nucleic acid that encodes atleast one TCE located within or flanking (e.g., juxtaposed to) theNS3/4A encoding fragment, such that the TCE is in a non-naturallyoccurring position. The encoded polypeptide retains catalytic activity(i.e., NS3 protease and/or NS3 helicase activity). Embodiments disclosedherein also provide chimeric NS3/4A polypeptides or fragments thereof ofat least 3 amino acids in length, which include a TCE within or flanking(e.g., juxtaposed to) the NS3/4A sequences, such that the TCE is in anon-naturally-occurring position.

Generally, the generation, enhancement, or improvement of an immuneresponse refers to an induction of a humoral (antibody) response and/ora cellular response. Most simply, an increase in the amount ofantigen-specific antibodies (e.g., total IgG) can be seen by utilizingone or more of the embodiments described herein. Enhancement of animmune response refers to any statistically significant change in thelevel of one or more immune cells (T cells, B cells, antigen-presentingcells, dendritic cells and the like) or in the activity of one or moreof these immune cells (cytotoxic T lymphocyte (CTL) activity, helper Tlymphocyte (HTL) activity, cytokine secretion, change in profile ofcytokine secretion). The skilled artisan will readily appreciate thatseveral methods for establishing whether an immune response isgenerated, enhanced, or improved are available. A variety of methods fordetecting the presence and levels of an immune response are available,for example. (See, e.g., Current Protocols in Immunology, Ed: John E.Coligan, et al. (2001) John Wiley & Sons, NY, N.Y.; Current Protocols inMolecular Biology, (2001), Greene Publ. Assoc. Inc. & John Wiley & Sons,NY, N.Y.; Ausubel et al. (2001) Current Protocols in Molecular Biology,Greene Publ. Assoc. Inc. & John Wiley & Sons, Inc., NY, N.Y.; Sambrooket al. (1989) Molecular Cloning, Second Ed., Cold Spring HarborLaboratory, Plainview, N.Y.); Maniatis et al. (1982) Molecular Cloning,Cold Spring Harbor Laboratory, Plainview, N.Y.; and elsewhere).Illustrative methods useful in this context include intracellularcytokine staining (ICS), ELISPOT, proliferation assays, cytotoxic T cellassays including chromium release or equivalent assays, and geneexpression analysis using any number of polymerase chain reaction (PCR)or RT-PCR based assays. For example, the number of CD8⁺ T-cells specificfor a particular antigen or TCE can be measured by flow cytometry. (See,e.g., Frelin et al. (2004) Gene Therapy 11:522-533). CTL priming canalso be measured in vivo by, for example, a tumor inhibition model, inwhich the ability of an animal (e.g., mouse) to inhibit growth of tumorsderived from tumor cells engineered to express the antigen of interest.Id.

In some embodiments, generation or enhancement of an immune responsecomprises an increase in target-specific CTL activity of between 1.5 and5 fold in a subject that is provided a composition that comprises thenucleic acids or polypeptides disclosed herein (e.g., in the context ofa chimeric NS3/4A nucleic acid or polypeptide), wherein the TCE isderived from the target, as compared to the same TCE that is notprovided in the context of the compositions disclosed herein. In someembodiments, an enhancement of an immune response comprises an increasein target-specific CTL activity of about 2, 2.5, 3, 3.5, 4, 4.5, 5, 5.5,6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5, 12, 12.5, 15, 16,17, 18, 19, 20, or more fold in a subject that is provided a compositionthat comprises a nucleic acid or a polypeptide disclosed herein (e.g.,in the context of a chimeric NS3/4A nucleic acid or polypeptide),wherein the TCE is derived from the target, as compared to as comparedto administration of the same TCE that is not provided in the context ofthe compositions disclosed herein.

In other embodiments, an alteration of an immune response comprises anincrease in target-specific HTL activity, such as proliferation ofhelper T cells, of between 1.5 and 5 fold in a subject that is provideda composition that comprises a nucleic acid or polypeptide disclosedherein (e.g., in the context of a chimeric NS3/4A nucleic acid orpolypeptide), wherein the TCE is derived from the target, as compared tothe same TCE that is not provided in the context of the compositionsdisclosed herein. In some embodiments, alteration of an immune responsecomprises an increase in target-specific HTL activity of about 2, 2.5,3, 3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11,11.5, 12, 12.5, 15, 16, 17, 18, 19, 20, or more fold in a subject thatis provided a composition that comprises a nucleic acid or polypeptidedisclosed herein (e.g., in the context of a chimeric NS3/4A nucleic acidor polypeptide), wherein the TCE is derived from the target, as comparedto administration of the same TCE that is not provided in the context ofthe compositions disclosed herein. In this context, an enhancement inHTL activity may comprise an increase as described above, or decrease,in production of a particular cytokine, such as interferon-gamma (IFNγ),interleukin-1 (IL-1), IL-2, IL-3, IL-6, IL-7, IL-12, IL-15, tumornecrosis factor-alpha (TNFα), granulocyte macrophage colony-stimulatingfactor (GM-CSF), granulocyte-colony stimulating factor (G-CSF), or othercytokine. In this regard, generation or enhancement of an immuneresponse may comprise a shift from a Th2 type response to a Th1 typeresponse or in certain embodiments a shift from a Th1 type response, toa Th2 type response. In other embodiments, the generation or enhancementof an immune response may comprise the stimulation of a predominantlyTh1 or a Th2 type response.

In still more embodiments, an increase in the amount of antibodyspecific for the antigen (e.g., total IgG) is increased. Someembodiments, for example, generate an increase in heterologoustarget-specific antibody production of between 1.5, 2, 3, 4, or 5 foldin a subject that is provided a composition comprising the nucleic acidsor polypeptides disclosed herein, (e.g., in the context of a chimericNS3/4A nucleic acid or polypeptide), wherein the TCE is derived from thetarget, as compared to the same TCE that is not present in the contextof the compositions disclosed herein. In some embodiments, the increasein heterologous target-specific antibody production is about 2, 2.5, 3,3.5, 4, 4.5, 5, 5.5, 6, 6.5, 7, 7.5, 8, 8.5, 9, 9.5, 10, 10.5, 11, 11.5,12, 12.5, 15, 16, 17, 18, 19, 20, or more fold in a subject that isprovided a composition that comprises a nucleic acid or polypeptidedisclosed herein, (e.g., in the context of a chimeric NS3/4A nucleicacid or polypeptide), wherein the TCE is derived from the target, ascompared to as compared to administration of the same TCE that is notpresent in the context of the compositions disclosed herein.

Generation or enhancement of a cellular immune response can also referto the frequency of cytotoxic T lymphocytes (CTLs) specific for adesired antigen that are primed, or the rapidity of priming of cytotoxicT lymphocytes (CTLs) specific for a desired antigen, compared to thepriming of CTLs specific for the desired epitope when the epitope is notpresented in the context of the nucleic acids or peptides disclosedherein. The section below describes several of the NS3/4A sequences thatcan be used in the compositions and methods described herein.

HCV Sequences

Several embodiments described herein provide genetic constructs thatcontain HCV sequences from the NS3/NS4A region of HCV. The NS3/NS4Aregion of HCV has been studied extensively. NS3, due to its limitedgenetic variability and relatively large size (631 amino acids) has initself been studied as an attractive target for generating immuneresponses against HCV. (See Bartenschlager R., et al. (1995) J. Virol.67:3835-3844; Pang et al. (2002) EMBO J. 21:1168-1176). The fact thatNS3 is a relatively large protein renders it less likely to exhibitgenetic non-responder status at the T cell level. (See Frelin et al.(2003) Gene Therapy 10:689-699). Accordingly, it was contemplated thatthe NS3 region of HCV is useful in genetic constructs for generating orenhancing an immune response to an accompanied target antigen (e.g., inconstructs that encode a TCE derived from a pathogen).

The catalytic activity of NS3 is known to affect a host's ability tomount an immune response to HCV. (See, e.g., Foy, et al. (2005), Proc.Nat. Acad. Sci. USA 102(8): 2986-2991; Meylan, et al. (2005) Nature437(20)1167-1172; Li et al. (2005) Proc. Nat. Acad. Sci. USA 102(8):2992-2997). Accordingly, embodiments described herein relate to geneticconstructs encoding catalytically active NS3/4A polypeptide derivatives,or functional fragments thereof, as well as the polypeptides encoded bythe genetic constructs. As used herein, the term “functional fragment”of a polypeptide refers to a variant of the polypeptide that is notfull-length yet retains desired attributes, (e.g. NS3A protease and/orhelicase activity, NS4A co-factor activity, or immunogenicity) of thefull-length native sequence.

The NS3 protein of HCV possesses both protease and helicase activity.(See Liu, D. et al., (2001) J. Mol. Biol. 314:543-561). In preferredembodiments, compositions disclosed herein include sequences that retainNS3 protease and/or helicase activity. In addition to cleaving the HCVpolypeptide, NS3 protease cleaves host proteins that normally functionto activate the host's innate immune response. (See, e.g., Foy, et al.(2005), Proc. Nat. Acad. Sci. USA 102(8): 2986-2991; Meylan, et al.(2005) Nature 437(20)1167-1172; Li et al. (2005) Proc. Nat. Acad. Sci.USA 102(8): 2992-2997). Specifically, NS3 has been shown to cleave theToll-like receptor 3 adaptor protein TRIF as well as Cardif. Id.Accordingly, in some embodiments, the NS3/4A nucleic acid sequencesencode a polypeptide that comprises an NS3 protease domain (e.g., asequence that exhibits protease activity).

NS3 protease activity is localized within the first 181 amino acids ofthe of NS3/4A peptide. (See, Lin, C. et al., (1994) J. Virol.68(12):8147-8157). The NS3 protease domain has a trypsin-like serineproteinase motif and a zinc binding site. (See, Love, R. (1996) Cell87:331-342). Three residues, His57, Asp81 and Ser139 constitute acatalytic triad typical of the trypsin-like serine proteases that arestrictly conserved in all HCV genotype sequences. Strict conservation ofspacing and order of these residues is also seen. The active site alsocontains an oxyanion/stabilization loop. The zinc binding site of NS3 islocated within amino acids Cys97, Cys99, Cys145 and His149. Id. The zincbinding site is more highly conserved than the active site and isresponsible for stabilizing the structure of the active site. Id.

The crystal structure HCV NS3 with an NS4A polypeptide has been solved.(See Yao, et al. (1999), Structure 7:1353-1363). Thus, where the NS3protease domain contains, for example, an alpha-helix or a beta-sheetstructure, in some embodiments, variants or modified NS3/4A moleculescomprise insertions of amino acids that maintain that specificstructure. In addition to the structural information above, we describeherein experimental results in which each and every residue in the NS3protease domain was systematically mutated and tested for proteaseactivity, thus providing guidance in relation to NS3/4A variants, suchas which amino acids in the NS3 protease domain are preferably preservedin embodiments that retain NS3 protease activity, as well as positionsalong the protease domain that can tolerate insertions of TCEs and/orTCEs and linkers, as discussed in more detail below.

As used herein the phrase “NS3 protease domain” refers to sequencesencoding the NS3 protease domain from any or all HCV genotypes orisotypes now known or discovered in the future. Nucleic acids encodingNS3 protease domains include any nucleic acid, taking into account thedegeneracy of the genetic code that encodes an NS3 protease domain, andalso including codon-optimized NS3 sequences and modified NS3 sequencesderived from naturally-occurring NS3 nucleic acids. Non-limitingexamples of NS3/4A nucleic acid sequences that can be used with theembodiments described herein include SEQ ID NOs: 1, 35, and 572-808. Byway of example, NS3 helicase domains can comprise nucleic acid residues1-551 of SEQ ID NO:35, or analogous residues in any NS3/4A nucleic acid.SEQ ID NO: 35 is an exemplary codon-optimized sequence of a nucleic acidencoding an NS3/NS4A protein generated from an HCV isolate.

The NS3 helicase domain resides in the C terminal 450 amino acids of theprotein. Yao et al. (1997) Nat. Struct. Biol. 4(6):463-467. Thestructure of the helicase domain by itself, in complex withsingle-stranded DNA, and in the bifunctional protease-helicase complexeswith NS4A has been solved. (Id. and Kim et al. (1998), Structure6:89-100). Previous studies have indicated that the protease domain ofNS3 enhances the helicase activity of NS3. (See, Frick et al. (2004) JBiol. Chem. 279(2):1269-1280). The available structural informationabove provide guidance as to the nature of NS3/4A variants, whichinclude substitutions, insertions and deletions in the NS3 helicasedomain that can be made without perturbing the catalytic activity of thehelicase domain, for example in embodiments that retain NS3 helicaseactivity.

As used herein, the phrase “NS3 helicase domain” refers to sequencesencoding an NS3 helicase domain from any or all HCV genotypes now knownor discovered in the future. Nucleic acids encoding NS3 helicase domainsinclude any nucleic acid, taking into account the degeneracy of thegenetic code that encodes an NS3 polypeptide and also includingcodon-optimized NS3 helicase sequences and modified NS3 helicasesequences derived from naturally-occurring NS3 helicase nucleic acids.Non-limiting examples of NS3/4A nucleic acid sequences, includingsequences of NS3 helicase domains, are SEQ ID NOs: 1, 35, and 572-808.By way of example, NS3 helicase domains can comprise nucleic acidresidues 218-1568 of SEQ ID NO:35, or analogous residues in any NS3/4Anucleic acid. SEQ ID NO: 35 is an exemplary codon-optimized nucleic acidsequence of an NS3/NS4A peptide generated from an HCV isolate.

The NS4 polypeptide of HCV has been shown to increase the intracellularstability of NS3 and target NS3 to intracellular membranes, therebypotentially increasing the immunogenicity of NS3. (See, Wolk, B. et al.(2000). J. Virol. 74:2293-2304). We recently demonstrated that NS4A genefrom HCV is an enhancer that increases transcription and immunogenicityof an associated gene or nucleic acid (e.g., NS3). (See, WO 04/048403,which designated the United States and was published in English, thedisclosure of which is hereby expressly incorporated by reference in itsentirety). The data illustrate that when HCV-1 NS3/4A was transfectedinto mammalian cells, vis a vis a eukaryotic expression vector, theexpression level of NS3 was increased compared to the expression levelsof NS3 alone (i.e., without NS4A). Further, immunization with anNS3/NS4A construct was shown to prime NS3-specific CTLs, when theconstruct was provided either i.m. or transdermally. Accordingly,embodiments disclosed herein include sequences encoding an NS4Apolypeptide, variant, or functional fragment thereof.

As used herein, the term “NS4A” refers to either nucleic acid or aminoacid sequences of the NS4A region from any and all HCV genotypes nowknown or discovered in the future. Nucleic acids encoding NS4A includeany nucleic acid, taking into account the degeneracy of the geneticcode, that encodes an NS4A domain and also includes codon-optimized NS4Asequences and modified NS4A sequences derived from naturally-occurringNS4A nucleic acids. Non-limiting examples of NS3/4A nucleic acidsequences, including sequences of NS4 co-factor domains, are SEQ ID NOs:1, 35, 567-804. By way of example, NS3 helicase domains can comprisenucleic acid residues 1569-2069 of SEQ ID NO:35, or analogous residuesin any NS3/4A nucleic acid. SEQ ID NO: 35 is an exemplarycodon-optimized nucleic acid sequence of an NS3/NS4A peptide generatedfrom an HCV isolate. SEQ ID NO:36 is an exemplary codon-optimized aminoacid sequence of an NS3/4A peptide generated from an HCV isolate.

Current listings of exemplary HCV nucleic acid and polypeptidesequences, including NS3/NS4A, are publicly available at the Los AlamosNational Laboratories world-wide web site. HCV NS3/4A nucleic acidsequences (including novel NS3/NS4A regions) can also be isolated frompatients infected with HCV using the nucleic acids described herein.(See also, Example 1). RNA obtained from a patient infected with HCV canbe reverse transcribed and the resultant cDNA can be amplified using PCRor another amplification technique. The primers are preferably obtainedfrom the NS3/4A sequence of SEQ. ID. NO.: 1.

For a review of PCR technology, see Molecular Cloning to GeneticEngineering White, B. A. Ed. in Methods in Molecular Biology 67: HumanaPress, Totowa (1997) and the publication entitled “PCR Methods andApplications” (1991, Cold Spring Harbor Laboratory Press). Foramplification of mRNAs, it is within the scope of the invention toreverse transcribe mRNA into cDNA followed by PCR (RT-PCR); or, to use asingle enzyme for both steps as described in U.S. Pat. No. 5,322,770.Another technique involves the use of Reverse Transcriptase AsymmetricGap Ligase Chain Reaction (RT-AGLCR), as described by Marshall R. L. etal. (PCR Methods and Applications 4:80-84, 1994).

Briefly, RNA is isolated, following standard procedures. A reversetranscription reaction is performed on the RNA using an oligonucleotideprimer specific for the most 5′ end of the amplified fragment as aprimer of first strand synthesis. The resulting RNA/DNA hybrid is then“tailed” with guanines using a standard terminal transferase reaction.The hybrid is then digested with RNAse H, and second strand synthesis isprimed with a poly-C primer. Thus, cDNA sequences upstream of theamplified fragment are easily isolated. For a review of cloningstrategies which can be used see e.g., Sambrook et al., 1989, supra.

In each of these amplification procedures, primers on either side of thesequence to be amplified are added to a suitably prepared nucleic acidsample along with dNTPs and a thermostable polymerase, such as Taqpolymerase, Pfu polymerase, or Vent polymerase. The nucleic acid in thesample is denatured and the primers are specifically hybridized tocomplementary nucleic acid sequences in the sample. The hybridizedprimers are then extended. Thereafter, another cycle of denaturation,hybridization, and extension is initiated. The cycles are repeatedmultiple times to produce an amplified fragment containing the nucleicacid sequence between the primer sites. PCR has further been describedin several patents including U.S. Pat. Nos. 4,683,195, 4,683,202 and4,965,188.

The primers are selected to be substantially complementary to a portionof the nucleic acid sequence of (SEQ. ID. NO.: 1) that is unique to thisNS3/4A molecule, thereby allowing the sequences between the primers tobe amplified. Preferably, primers can be any number between at least16-20, 20-25, or 25-30 nucleotides in length. The formation of stablehybrids depends on the melting temperature (Tm) of the DNA. The Tmdepends on the length of the primer, the ionic strength of the solutionand the G+C content. The higher the G+C content of the primer, thehigher is the melting temperature because G:C pairs are held by three Hbonds whereas A:T pairs have only two. The G+C content of theamplification primers described herein preferably range between 10% and75%, more preferably between 35% and 60%, and most preferably between40% and 55%. The appropriate length for primers under a particular setof assay conditions can be empirically determined by one of skill in theart.

The spacing of the primers relates to the length of the segment to beamplified. In the context of the embodiments described herein, amplifiedsegments carrying nucleic acid sequence encoding HCV peptides can rangein size from at least about 25 bp to the entire length of the HCVgenome. Amplification fragments from 25-1000 bp are typical, fragmentsfrom 50-1000 bp are preferred and fragments from 100-600 bp are highlypreferred. It will be appreciated that amplification primers can be ofany sequence that allows for specific amplification of the NS3/4A regionand can, for example, include modifications such as restriction sites tofacilitate cloning.

The PCR product can be subcloned and sequenced to ensure that theamplified sequences represent the sequences of an HCV peptide. The PCRfragment can then be used to isolate a full length cDNA clone by avariety of methods. For example, the amplified fragment can be labeledand used to screen a cDNA library, such as a bacteriophage cDNA library.Alternatively, the labeled fragment can be used to isolate genomicclones via the screening of a genomic library. Additionally, anexpression library can be constructed utilizing cDNA synthesized from,for example, RNA isolated from an infected patient. In this manner, HCVgene products can be isolated using standard antibody screeningtechniques in conjunction with antibodies raised against the HCV geneproduct. (For screening techniques, see, for example, Harlow, E. andLane, eds., 1988, Antibodies: A Laboratory Manual, Cold Spring HarborPress, Cold Spring Harbor).

NS3/NS4A Variant Sequences

A novel nucleic acid and protein corresponding to the NS3/4A domain ofHCV was cloned from a patient infected with HCV (SEQ. ID. NO.: 1). AGenebank search revealed that the cloned sequence had the greatesthomology to HCV sequences but was only 93% homologous to the closest HCVrelative (accession no AJ 278830). This novel peptide (SEQ. ID. NO.: 2)and fragments thereof (e.g., SEQ. ID. NOs.: 14 and 15) that are anynumber of consecutive amino acids between at least 3-50 (e.g., 3, 4, 6,8, 10, 12, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids in length),nucleic acids encoding these molecules, vectors having said nucleicacids, and cells having said vectors, nucleic acids, or peptides areembodiments of the invention. It was also discovered that both theNS3/4A gene (SEQ. ID. NO.: 1) and corresponding peptide (SEQ. ID. NO.:2) were immunogenic in vivo.

In certain embodiments, the NS3/4A nucleic acids and polypeptides of thecompositions and methods disclosed herein include variations innucleotide and/or amino acid sequences, compared to native NS3/4Asequences and are referred to as NS3/4A variants. As used herein, theterm “native” refers to naturally occurring HCV sequences (e.g.,available HCV isotypes). Variants may include a substitution, deletionor insertion of one or more nucleotides, amino acids, or codons encodingthe NS3/4A sequences of the chimeric NS3/4A polypeptides, which resultsin a change in the amino acid sequence of the NS3/4A polypeptide, ascompared with the native sequence. Variants can be engineered, forexample, using any of the techniques and guidelines for conservative andnon-conservative mutations set forth, for instance, in U.S. Pat. No.5,364,934.

Mutants of the novel NS3/4A peptide were created. It was discovered thattruncated mutants (e.g., SEQ. ID. NOs.: 12 and 13) and mutants that lacka proteolytic cleavage site (SEQ. ID. NOs.: 3-11), were also immunogenicin vivo. These novel peptides (SEQ. ID. NOs.: 3-13) and fragmentsthereof (e.g., SEQ. ID. NOs.: 16-26) that are any number of consecutiveamino acids between at least 3-50 (e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25,30, 35, 40, 45, or 50 amino acids in length), nucleic acids encodingthese molecules, vectors having said nucleic acids, and cells havingsaid vectors, nucleic acids, or peptides are also embodiments of theinvention.

A codon-optimized nucleic acid encoding NS3/4a was also created and wasfound to be immunogenic. The nucleic acid of SEQ. ID. NO.: 1 wasanalyzed for codon usage and the sequence was compared to the codonsthat are most commonly used in human cells. Because HCV is a humanpathogen, it was unexpected to discover that the virus had not yetevolved to use codons that are most frequently found to encode humanproteins (e.g., optimal human codons). A total of 435 nucleotides werereplaced to generate the codon-optimized synthetic NS3/4A nucleic acid.The NS3/4A peptide encoded by the codon-optimized nucleic acid sequence(SEQ. ID. NO.: 36) was 98% homologous to HCV-1 and contained a total of15 different amino acids.

The codon optimized nucleic acid (MSLF1 or coNS3/4A) (SEQ. ID. NO.: 35)was found to be more efficiently translated in vitro than the nativeNS3/4A and that mice immunized with the MSLF1 containing constructgenerated significantly more NS3/4A specific antibodies than miceimmunized with a wild-type NS3/4A containing construct. Further, miceimmunized with the MSLF1 containing construct were found to primeNS3-specific CTLs more effectively and exhibit better in vivo tumorinhibiting immune responses than mice immunized with wild-type NS3/4Acontaining constructs.

NS3/NS4A genes encoding polypeptides with alanine or glycinesubstitutions in the serine protease domain of NS3 (i.e., the first 181amino acids) (SEQ ID NO's: 40 through 220 and 1329-1339) were found tohave altered protease activity compared to the wtNS3/NS4A polypeptide.

The peptides and nucleic acids described above are useful as immunogens,which can be administered alone or in conjunction with an adjuvant.Preferred embodiments include compositions that comprise one or more ofthe nucleic acids and/or peptides described above with or without anadjuvant. That is, some of the compositions described herein areprepared with or without an adjuvant and comprise, consist, or consistessentially of a NS3/4A peptide (SEQ. ID. NO.: 2 or SEQ. ID. NO.: 36) orfragments thereof that are any number of consecutive amino acids betweenat least 3-50 (e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, or50 amino acids in length) (e.g., SEQ. ID. NOs.: 14 and 15) or a nucleicacid encoding one or more of these molecules (e.g., SEQ. ID. NO.: 35) ora fragment thereof that is any number of consecutive nucleotides betweenat least 12-2112 (e.g., 12-15, 15-20, 20-30, 30-50, 50-100, 100-200,200-500, 500-1000, 1000-1500, 1500-2079, or 1500-2112 consecutivenucleotides in length). Additional compositions are prepared with orwithout an adjuvant and comprise, consist, or consist essentially of oneor more of the NS3/4A mutant peptides (SEQ. ID. NOs.: 3-13) andfragments thereof that are any number of consecutive amino acids betweenat least 3-50 (e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40, 45, or50 amino acids in length). Some of the compositions described herein areprepared with or without an adjuvant and comprise, consist, or consistessentially of a mutant NS3/NS4A peptide (e.g., SEQ ID NO's: 40 through220 and 1329-1339), or a nucleic acid encoding one or more of thesemolecules.

It was also discovered that compositions comprising ribavirin and anantigen (e.g., one or more of the previously described HCV peptides ornucleic acids) enhance and/or facilitate an animal's immune response tothe antigen. That is, it was discovered that ribavirin is a veryeffective “adjuvant,” which for the purposes of this disclosure, refersto a material that has the ability to enhance or facilitate an immuneresponse to a particular antigen. The adjuvant activity of ribavirin wasmanifested by a significant increase in immune-mediated protectionagainst the antigen, an increase in the titer of antibody raised to theantigen, and an increase in proliferative T cell responses.

Accordingly, compositions (e.g., vaccines and other medicaments) thatcomprise ribavirin and one or more of the peptides or nucleic acidsdescribed herein are embodiments of the invention. These compositionscan vary according to the amount of ribavirin, the form of ribavirin, aswell as the sequence of the HCV nucleic acid or peptide.

Embodiments of the invention also include methods of making and usingthe compositions above. Some methods involve the making of nucleic acidsencoding NS3/4A, codon-optimized NS3/4A, mutant NS34A, fragments thereofthat are any number of consecutive nucleotides between at least 9-100(e.g., 9, 12, 15, 18, 21, 24, 27, 30, 50, 60, 75, 80, 90, or 100consecutive nucleotides in length), peptides corresponding to saidnucleic acids, constructs comprising said nucleic acids, and cellscontaining said compositions. Preferred methods, however, concern themaking of vaccine compositions or immunogenic preparations thatcomprise, consist, or consist essentially of the newly discovered NS3/4Afragment, codon-optimized NS3/4A, or an NS3/4A mutant (e.g., a truncatedmutant, a mutant lacking a proteolytic cleavage site, or a mutant havingaltered protease activity), or a fragment thereof or a nucleic acidencoding one or more of these molecules, as described above. Preferredfragments for use with the methods described herein include SEQ. ID.NOs.: 12-27 and fragments of SEQ. ID. NO.: 35 that contain at least 30consecutive nucleotides. The compositions described above can be made byproviding an adjuvant (e.g., ribavirin), providing an HCV antigen (e.g.,a peptide comprising an HCV antigen such as (SEQ. ID. NOs.: 2-11, 36, or40-220) or a fragment thereof such as, SEQ. ID. NOs.: 12-26 or a nucleicacid encoding one or more of said peptides), and mixing said adjuvantand said antigen so as to formulate a composition that can be used toenhance or facilitate an immune response in a subject to said antigen.

Methods of enhancing or promoting an immune response in an animal,including humans, to an antigen are also provided. Such methods can bepracticed, for example, by identifying an animal in need of an immuneresponse to HCV and providing said animal a composition comprising oneor more of the nucleic acids or peptides above and an amount of adjuvantthat is effective to enhance or facilitate an immune response to theantigen/epitope. In some embodiments, the antigen and the adjuvant areadministered separately, instead of in a single mixture. Preferably, inthis instance, the adjuvant is administered a short time before or ashort time after administering the antigen. Preferred methods involveproviding the animal in need with ribavirin and NS3/4A (e.g., SEQ. ID.NO.: 2), codon-optimized NS3/4A (e.g., SEQ. ID. NO.: 36), a mutantNS3/4A (e.g., SEQ. ID. NOs.: 3-13 or 40-220), a fragment thereof (e.g.,SEQ. ID. NOs.: 14-26) containing any number of consecutive amino acidsbetween at least 3-50 (e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35, 40,45, or 50 amino acids in length) or a nucleic acid encoding any one ormore of said molecules.

Other embodiments concern methods of treating and preventing HCVinfection. By one approach, an immunogen comprising one or more of theHCV nucleic acids or peptides described herein are used to prepare amedicament for the treatment and/or prevention of HCV infection. Byanother approach, an individual in need of a medicament that preventsand/or treats HCV infection is identified and said individual isprovided a medicament comprising ribavirin and an HCV antigen such asNS3/4A (e.g., SEQ. ID. NO.: 2), codon-optimized NS3/4A (e.g., SEQ. ID.NO.: 36), or a mutant NS3/4A (e.g., SEQ. ID. NOs.: 3-13 or 40-220), afragment thereof (e.g., SEQ. ID. NOs.: 14-26) containing any number ofconsecutive amino acids between at least 3-50 (e.g., 3, 4, 6, 8, 10, 12,15, 20, 25, 30, 35, 40, 45, or 50 amino acids in length) or a nucleicacid encoding any one or more of these molecules.

The section below discusses the discovery of the novel NS3/4A gene, thecodon-optimized NS3/4A gene, the creation of the NS3/4A mutants, and thecharacterization of the nucleic acids and peptides correspondingthereto.

NS3/4A, NS3/4A Mutants, and Codon-Optimized NS3/4A

A novel nucleic acid and protein corresponding to the NS3/4A domain ofHCV was cloned from a patient infected with HCV (SEQ. ID. NOs.: 1 and2). A Genebank search revealed that the cloned sequence had the greatesthomology to HCV sequences but was only 93% homologous to the closest HCVrelative (accession no AJ 278830). A truncated mutant of the novelNS3/4A peptide and NS3/4A mutants, which lack a proteolytic cleavagesite, (as well as corresponding nucleic acids) were also created.Further, a human codon-optimized NS3/4A nucleic acid and peptide werecreated. It was discovered that these novel peptides and nucleic acidsencoding said peptides were potent immunogens that can be mixed withadjuvants so as to make a composition that induces a recipient toprovide an immune response to HCV. The cloning of the novel NS3/4A geneand the creation of the various NS3/4A mutants and codon optimizedNS3/4A gene are described in the following example.

Example 1

The NS3/4A sequence was amplified from the serum of an HCV-infectedpatient (HCV genotype 1a) using the Polymerase Chain Reaction (PCR).Total RNA was extracted from serum, and cDNA synthesis and PCR wereperformed according to standard protocols (Chen M et al., J. Med. Virol.43:223-226 (1995)). The cDNA synthesis was initiated using the antisenseprimer “NS4KR” (5′-CCG TCT AGA TCA GCA CTC TTC CAT TTC ATC-3′ (SEQ. ID.NO.: 28)). From this cDNA, a 2079 base pair DNA fragment of HCV,corresponding to amino acids 1007 to 1711, which encompasses the NS3 andNS4A genes, was amplified. A high fidelity polymerase (Expand HighFidelity PCR, Boehringer-Mannheim, Mannheim, Germany) was used with the“NS3KF” primer (5′-CCT GAA TTC ATG GCG CCT ATC ACG GCC TAT-3′ (SEQ. ID.NO.: 29) and the NS4KR primer. The NS3KF primer contained a EcoRIrestriction enzyme cleavage site and a start codon and the primer NS4KRcontained a XbaI restriction enzyme cleavage site and a stop codon.

The amplified fragment was then sequenced (SEQ. ID. NO.: 1). Sequencecomparison analysis revealed that the gene fragment was amplified from aviral strain of genotype 1a. A computerized BLAST search against theGenbank database using the NCBI website revealed that the closest HCVhomologue was 93% identical in nucleotide sequence.

The amplified DNA fragment was then digested with EcoRI and XbaI, andwas inserted into a pcDNA3.1/His plasmid (Invitrogen) digested with thesame enzymes. The NS3/4A-pcDNA3.1 plasmid was then digested with EcoRIand Xba I and the insert was purified using the QiaQuick kit (Qiagen,Hamburg, Germany) and was ligated to a EcoRI/Xba I digested pVAX vector(Invitrogen) so as to generate the NS3/4A-pVAX plasmid.

The rNS3 truncated mutant was obtained by deleting NS4A sequence fromthe NS3/4A DNA. Accordingly, the NS3 gene sequence of NS3/4A-pVAX wasPCR amplified using the primers NS3KF and 3′ NotI (5′-CCA CGC GGC CGCGAC GAC CTA CAG-3′ (SEQ. ID. NO.: 30)) containing EcoRI and Not Irestriction sites, respectively. The NS3 fragment (1850 bp) was thenligated to a EcoRI and Not I digested pVAX plasmid to generate theNS3-pVAX vector. Plasmids were grown in BL21 E. coli cells. The plasmidswere sequenced and were verified by restriction cleavage and the resultswere as to be expected based on the original sequence.

In some embodiments, nucleic acid sequences comprising, consistingessentially of, or consisting of sequences encoding TCEs are insertedwithin or flanking (e.g., juxtaposed to) the NS3/4A-encoding sequencedescribed herein. In some embodiments, a linker or adjuvant sequence isalso, optionally, inserted within or flanking (e.g., juxtaposed to) anNS3/4A native or variant sequence, or a native or variant TCE sequence.For example, the chimeric NS3/4A polypeptide encoded by the nucleicacids above can include sequences encoding a TCE, or a TCE flanked onone or both sides by linkers and/or adjuvant sequences, inserted betweenamino acids 1 and 2, 2 and 3, 3 and 4, 4 and 5, 5 and 6, 6 and 7, 7 and8, 8 and 9, 9 and 10, 10 and 11, 11 and 12, 12 and 13, 13 and 14, 14 and15, 15 and 16, 16 and 17, 17 and 18, 18 and 19, 19 and 20, 20 and 21, 21and 22, 22 and 23, 23 and 24, 24 and 25, 25 and 26, 26 and 27, 27 and28, 28 and 29, 29 and 30, 30 and 31, 31 and 32, 32 and 33, 33 and 34, 34and 35, 35 and 36, 36 and 37, 37 and 38, 38 and 39, 39 and 40, 40 and41, 41 and 42, 42 and 43, 43 and 44, 44 and 45, 45 and 46, 46 and 47, 47and 48, 48 and 49, 49 and 50, 50 and 51, 51 and 52, 52 and 53, 53 and54, 54 and 55, 55 and 56, 56 and 57, 57 and 58, 58 and 59, 59 and 60, 60and 61, 61 and 62, 62 and 63, 63 and 64, 64 and 65, 65 and 66, 66 and67, 67 and 68, 68 and 69, 69 and 70, 70 and 71, 71 and 72, 72 and 73, 73and 74, 74 and 75, 75 and 76, 76 and 77, 77 and 78, 78 and 79, 79 and80, 80 and 81, 81 and 82, 82 and 83, 83 and 84, 84 and 85, 85 and 86, 86and 87, 87 and 88, 88 and 89, 89 and 90, 90 and 91, 91 and 92, 92 and93, 93 and 94, 94 and 95, 95 and 96, 96 and 97, 97 and 98, 98 and 99, 99and 100, 100 and 101, 101 and 102, 102 and 103, 103 and 104, 104 and105, 105 and 106, 106 and 107, 107 and 108, 108 and 109, 109 and 110,110 and 111, 111 and 112, 112 and 113, 113 and 114, 114 and 115, 115 and116, 116 and 117, 117 and 118, 118 and 119, 119 and 120, 120 and 121,121 and 122, 122 and 123, 123 and 124, 124 and 125, 125 and 126, 126 and127, 127 and 128, 128 and 129, 129 and 130, 130 and 131, 131 and 132,132 and 133, 133 and 134, 134 and 135, 135 and 136, 136 and 137, 137 and138, 138 and 139, 139 and 140, 140 and 141, 141 and 142, 142 and 143,143 and 144, 144 and 145, 145 and 146, 146 and 147, 147 and 148, 148 and149, 149 and 150, 150 and 151, 151 and 152, 152 and 153, 153 and 154,154 and 155, 155 and 156, 156 and 157, 157 and 158, 158 and 159, 159 and160, 160 and 161, 161 and 162, 162 and 163, 163 and 164, 164 and 165,165 and 166, 166 and 167, 167 and 168, 168 and 169, 169 and 170, 170 and171, 171 and 172, 172 and 173, 173 and 174, 174 and 175, 175 and 176,176 and 177, 177 and 178, 178 and 179, 179 and 180, 180 and 181, 181 and182, 182 and 183, 183 and 184, 184 and 185, 185 and 186, 186 and 187,187 and 188, 188 and 189, 189 and 190, 190 and 191, 191 and 192, 192 and193, 193 and 194, 194 and 195, 195 and 196, 196 and 197, 197 and 198,198 and 199, 199 and 200, 200 and 201, 201 and 202, 202 and 203, 203 and204, 204 and 205, 205 and 206, 206 and 207, 207 and 208, 208 and 209,209 and 210, 210 and 211, 211 and 212, 212 and 213, 213 and 214, 214 and215, 215 and 216, 216 and 217, 217 and 218, 218 and 219, 219 and 220,220 and 221, 221 and 222, 222 and 223, 223 and 224, 224 and 225, 225,and 226, 226 and 227, 227 and 228, 228 and 229, 229 and 230, 230 and231, 231 and 232, 232 and 233, 233 and 234, 234 and 235, 235 and 236,236 and 237, 237 and 238, 238 and 239, 239 and 240, 240 and 241, 241 and242, 242 and 243, 243 and 244, 244 and 245, 245 and 246, 246 and 247,247 and 248, 248 and 249, 249 and 250, 250 and 251, 251 and 252, 252 and253, 253 and 254, 254 and 255, 255 and 256, 256 and 257, 257 and 258,258 and 259, 259 and 260, 260 and 261, 261 and 262, 262 and 263, 263 and264, 264 and 265, 265 and 266, 266 and 267, 267 and 268, 268 and 269,269 and 270, 270 and 271, 271 and 272, 272 and 273, 273 and 274, 274 and275, 275 and 276, 276 and 277, 277 and 278, 278 and 279, 279 and 280,280 and 281, 281 and 282, 282 and 283, 283 and 284, 284 and 285, 285 and286, 286 and 287, 287 and 288, 288 and 289, 289 and 290, 290 and 291,291 and 292, 292 and 293, 293 and 294, 294 and 295, 295 and 296, 296 and297, 297 and 298, 298 and 299, 299 and 300, 300 and 201, 301 and 302,302 and 303, 303 and 304, 304 and 305, 305 and 306, 306 and 307, 307 and308, 308 and 309, 309 and 310, 310 and 311, 311 and 312, 312 and 313,313 and 314, 314 and 315, 315 and 316, 316 and 317, 317 and 318, 318 and319, 319 and 320, 320 and 321, 321, and 322, 322 and 323, 323 and 324,324 and 325, 325, and 326, 326 and 327, 327 and 328, 328 and 329, 329and 330, 330 and 331, 331 and 332, 332 and 333, 333 and 334, 334 and335, 335 and 336, 336 and 337, 337 and 338, 338 and 339, 339 and 340,340 and 341, 341 and 342, 342 and 343, 343 and 344, 344 and 345, 345 and346, 346 and 347, 347 and 348, 348 and 349, 349 and 350, 350 and 351,351 and 352, 352 and 353, 353 and 354, 354 and 355, 355 and 356, 356 and357, 357 and 358, 358 and 359, 359 and 360, 360 and 361, 361 and 362,362 and 363, 363 and 364, 364 and 365, 365 and 366, 366 and 367, 367 and368, 368 and 369, 369 and 370, 370 and 371, 371 and 372, 372 and 373,373 and 374, 374 and 375, 375 and 376, 376 and 377, 377 and 378, 378 and379, 379 and 380, 380 and 381, 381 and 382, 382 and 383, 383 and 384,384 and 385, 385 and 386, 386 and 387, 387 and 388, 388 and 389, 389 and390, 390 and 391, 391 and 392, 392 and 393, 393 and 394, 394 and 395,395 and 396, 396 and 397, 397 and 398, 398 and 399, 399 and 400, 401 and402, 402 and 403, 403 and 404, 404 and 405, 405 and 406, 406 and 407,407 and 408, 408 and 409, 409 and 410, 410 and 411, 411 and 412, 412 and413, 413 and 414, 414 and 415, 415 and 416, 416 and 417, 417 and 418,418 and 419, 419 and 420, 420 and 421, 421 and 422, 422 and 423, 423 and424, 424 and 425, 425 and 426, 426 and 427, 427 and 428, 428 and 429,429 and 430, 430 and 431, 431 and 432, 432 and 433, 433 and 434, 434 and435, 435 and 436, 436 and 437, 437 and 438, 438 and 439, 439 and 440,440 and 441, 441 and 442, 442 and 443, 443 and 444, 444 and 445, 445 and446, 446 and 447, 447 and 448, 448 and 449, 449 and 450, 450 and 451,451 and 452, 452 and 453, 453 and 454, 454 and 455, 455 and 456, 456 and457, 457 and 458, 458 and 459, 459 and 460, 460 and 461, 461 and 462,462 and 463, 463 and 464, 464 and 465, 465 and 466, 466 and 467, 467 and468, 468 and 469, 469 and 470, 470 and 471, 471 and 472, 472 and 473,473 and 474, 474 and 475, 475 and 476, 476 and 477, 477 and 478, 478 and479, 479 and 480, 480 and 481, 481 and 482, 482 and 483, 483 and 484,484 and 485, 485 and 486, 486 and 487, 487 and 488, 488 and 489, 489 and490, 490 and 491, 491 and 492, 492 and 493, 493 and 494, 494 and 495,495 and 496, 496 and 497, 497 and 498, 498 and 499, 499 and 500, 501 and502, 502 and 503, 503 and 504, 504 and 505, 505 and 506, 506 and 507,507 and 508, 508 and 509, 509 and 510, 510 and 511, 511 and 512, 512 and513, 513 and 514, 514 and 515, 515 and 516, 516 and 517, 517 and 518,518 and 519, 519 and 520, 520 and 521, 521 and 522, 522 and 523, 523 and524, 524 and 525, 525 and 526, 526 and 527, 527 and 528, 528 and 529,529 and 530, 530 and 531, 531 and 532, 532 and 533, 533 and 534, 534 and535, 535 and 536, 536 and 537, 537 and 538, 538 and 539, 539 and 540,540 and 541, 541 and 542, 542 and 543, 543 and 544, 544 and 545, 545 and546, 546 and 547, 547 and 548, 548 and 549, 549 and 550, 550 and 551,551 and 552, 552 and 553, 553 and 554, 554 and 555, 555 and 556, 556 and557, 557 and 558, 558 and 559, 559 and 560, 560 and 561, 561 and 562,562 and 563, 563 and 564, 564 and 565, 565 and 566, 566 and 567, 567 and568, 568 and 569, 569 and 570, 570 and 571, 571 and 572, 572 and 573,573 and 574, 574 and 575, 575 and 576, 576 and 577, 577 and 578, 578 and579, 579 and 580, 580 and 581, 581 and 582, 582 and 583, 583 and 584,584 and 585, 585 and 586, 586 and 587, 587 and 588, 588 and 589, 589 and590, 590 and 591, 591 and 592, 592 and 593, 593 and 594, 594 and 595,595 and 596, 596 and 597, 597 and 598, 598 and 599, 599 and 600, 601 and602, 602 and 603, 603 and 604, 604 and 605, 605 and 606, 606 and 607,607 and 608, 608 and 609, 609 and 610, 610 and 611, 611 and 612, 612 and613, 613 and 614, 614 and 615, 615 and 616, 616 and 617, 617 and 618,618 and 619, 619 and 620, 620 and 621, 621 and 622, 622 and 623, 623 and624, 624 and 625, 625 and 626, 626 and 627, 627 and 628, 628 and 629,629 and 630, 630 and 631, 631 and 632, 632 and 633, 633 and 634, 634 and635, 635 and 636, 636 and 637, 637 and 638, 638 and 639, 639 and 640,640 and 641, 641 and 642, 642 and 643, 643 and 644, 644 and 645, 645 and646, 646 and 647, 647 and 648, 648 and 649, 649 and 650, 650 and 651,651 and 652, 652 and 653, 653 and 654, 654 and 655, 655 and 656, 656 and657, 657 and 658, 658 and 659, 659 and 660, 660 and 661, 661 and 662,662 and 663, 663 and 664, 664 and 665, 665 and 666, 666 and 667, 667 and668, 668 and 669, 669 and 670, 670 and 671, 671 and 672, 72 and 673, 673and 674, 674 and 675, 675 and 676, 676 and 677, 677 and 678, 678 and679, 679 and 680, 680 and 681, 681 and 682, 682 and 683, 683 and 684,684 and 685, or 685 and 686 of a variant NS3/4A polypeptide (e.g., SEQID NO: 36). For example, in preferred embodiments, the chimeric NS3/4Apolypeptide encoded by the nucleic acids above can include sequencesencoding a TCE, or a TCE flanked on one or both sides by linkers and/oradjuvant sequences, inserted between amino acids 453-513 of SEQ IDNO:36, or in an analogous position in any NS3/4A polypeptide.Embodiments also relate to the polypeptides encoded by said nucleicacids.

Accordingly, in some embodiments a nucleic acid encoding a TCE or a TCEand a linker(s) is inserted between the codons of an NS3/4A-encodingnucleic acid sequence. For example, in some embodiments, a nucleic acidencoding a TCE or a TCE and a linker(s) and/or an adjuvant sequence isinserted between nucleotides 3 and 4, 6 and 7, 9 and 10, 12 and 13, 15and 16, 18 and 19, 21 and 22, 24 and 25, 27 and 28, 30 and 31, 33 and34, 36 and 37, 39 and 40, 42 and 43, 45 and 46, 48 and 49, 51 and 52, 54and 55, 57 and 58, 60 and 61, 63 and 64, 66 and 67, 69 and 70, 72 and73, 75 and 76, 78 and 79, 81 and 82, 84 and 85, 87 and 88, 90 and 91, 93and 94, 96 and 97, 99 and 100, 102 and 103, 105 and 106, 108 and 109,111 and 112, 114 and 115, 117 and 118, 120 and 121, 123 and 124, 126 and127, 129 and 130, 132 and 133, 125 and 136, 138 and 139, 141 and 142,144 and 145, 147 and 148, 150 and 151, 153 and 154, 156 and 157, 159 and160, 162 and 163, 165 and 166, 168 and 169, 171 and 172, 174 and 175,177 and 178, 180 and 181, 183 and 184, 186 and 187, 189 and 19, 192 and193, 195 and 196, 198 and 199, 201 and 202, 204 and 205, 207 and 208,210 and 211, 213 and 214, 216 and 217, 219 and 220, 222 and 223, 225 and226, 228 and 229, 231 and 232, 234 and 235, 237 and 238, 240 and 241,243 and 244, 246 and 247, 249 and 250, 252 and 253, 255 and 256, 258 and259, 261 and 262, 264 and 265, 267 and 268, 270 and 271, 273 and 274,276 and 277, 279 and 280, 282 and 283, 285 and 286, 288 and 289, 291 and292, 294 and 295, 297 and 298, 300 and 301, 303 and 304, 306 and 307,309 and 310, 312 and 313, 315 and 316, 318 and 319, 321 and 322, 324 and325, 327 and 328, 330 and 331, 333 and 334, 336 and 337, 339 and 340,342 and 343, 345 and 346, 348 and 349, 351 and 352, 354 and 355, 357 and358, 360 and 361, 363 and 364, 366 and 367, 369 and 370, 372 and 373,375 and 376, 378 and 379, 381 and 382, 24 and 385, 387 and 388, 390 and391, 393 and 394, 396 and 397, 399 and 400, 402 and 403, 405 and 406,408 and 409, 411 and 412, 414 and 415, 417 and 418, 420 and 421, 423 and424, 426 and 427, 429 and 430, 432 and 433, 435 and 436, 438 and 439,441 and 442, 444 and 445, 447 and 448, 450 and 451, 453 and 454, 456 and457, 459 and 460, 462 and 463, 465 and 466, 468 and 469, 471 and 472,474 and 475, 477 and 478, 480 and 481, 483 and 484, 486 and 487, 489 and490, 492 and 493, 495 and 496, 498 and 499, 501 and 502, 504 and 505,507 and 508, 510 and 511, 513 and 514, 516 and 517, 519 and 520, 522 and523, 525 and 526, 528 and 529, 531 and 532, 534 and 535, 537 and 538,540 and 541, 543 and 544, 546 and 547, 549 and 550, 552 and 553, 555 and556, 558 and 559, 561 and 562, 564 and 565, 567 and 568, 570 and 571,573 and 574, 576 and 577, 579 and 580, 582 and 583, 585 and 586, 588 and589, 591 and 592, 594 and 595, 597 and 598, 600 and 601, 603 and 604,606 and 607, 609 and 610, 612 and 613, 615 and 616, 618 and 619, 621 and622, 624 and 625, 627 and 628, 630 and 631, 633 and 634, 636 and 637,639 and 640, 642 and 643, 645 and 646, 648 and 649, 651 and 652, 654 and655, 657 and 658, 660 and 661, 663 and 664, 666 and 667, 669 and 670,672 and 673, 675 and 676, 678 and 679, 681 and 682, 684 and 685, 687 and688, 690 and 691, 693 and 694, 696 and 697, 699 and 700, 702 and 703,705 and 706, 708 and 709, 711 and 712, 714 and 715, 717 and 718, 720 and721, 723 and 724, 726 and 727, 729 and 730, 732 and 733, 735 and 736,738 and 739, 741 and 742, 744 and 745, 747 and 748, 750 and 751, 753 and754, 756 and 757, 759 and 760, 762 and 763, 765 and 766, 768 and 769,771 and 772, 774 and 775, 777 and 778, 780 and 781, 783 and 784, 786 and787, 789 and 790, 792 and 793, 795 and 796, 798 and 799, 801 and 802,804 and 805, 807 and 808, 810 and 811, 813 and 814, 816 and 817, 819 and820, 822 and 823, 825 and 826, 828 and 829, 831 and 832, 834 and 835,837 and 838, 840 and 841, 843 and 844, 846 and 847, 849 and 850, 852 and853, 855 and 856, 858 and 859, 861 and 862, 864 and 865, 867 and 868,870 and 871, 873 and 874, 876 and 877, 879 and 880, 882 and 883, 885 and886, 888 and 889, 891 and 892, 894 and 895, 897 and 898, 900 and 901,903 and 904, 906 and 907, 909 and 910, 912 and 913, 915 and 916, 918 and919, 921 and 922, 924 and 925, 927 and 928, 930 and 931, 933 and 934,936 and 937, 939 and 940, 942 and 943, 945 and 946, 948 and 949, 951 and952, 954 and 955, 957 and 958, 960 and 961, 963 and 964, 966 and 967,969 and 970, 972 and 973, 975 and 976, 978 and 979, 981 and 982, 984 and985, 987 and 988, 990 and 991, 993 and 994, 996 and 997, 999 and 1000,1002 and 1003, 1005 and 1006, 1008 and 1009, 1011 and 1012, 1014 and1015, 1017 and 1018, 1020 and 1021, 1023 and 1024, 1026 and 1027, 1029and 1030, 1032 and 1033, 1025 and 1036, 1038 and 1039, 1041 and 1042,1044 and 1045, 1047 and 1048, 1050 and 1051, 1053 and 1054, 1056 and1057, 1059 and 1060, 1062 and 1063, 1065 and 1066, 1068 and 1069, 1071and 1072, 1074 and 1075, 1077 and 1078, 1080 and 1081, 1083 and 1084,1086 and 1087, 1089 and 1090, 1092 and 1093, 1095 and 1096, 1098 and1099, 1101 and 1102, 1104 and 1105, 1107 and 1108, 1110 and 1111, 1113and 1114, 1116 and 1117, 1119 and 1120, 1122 and 1123, 1125 and 1126,1128 and 1129, 1131 and 1132, 1134 and 1135, 1137 and 1138, 1140 and1141, 1143 and 1144, 1146 and 1147, 1149 and 1150, 1152 and 1153, 1155and 1156, 1158 and 1159, 1161 and 1162, 1164 and 1165, 1167 and 1168,1170 and 1171, 1173 and 1174, 1176 and 1177, 1179 and 1180, 1182 and1183, 1185 and 1186, 1188 and 1189, 1191 and 1192, 1194 and 1195, 1197and 1198, 1200 and 1201, 1203 and 1204, 1206 and 1207, 1209 and 1210,1212 and 1213, 1215 and 1216, 1218 and 1219, 1221 and 1222, 1224 and1225, 1227 and 1228, 1230 and 1231, 1233 and 1234, 1236 and 1237, 1239and 1240, 1242 and 1243, 1245 and 1246, 248 and 1249, 1251 and 1252,1254 and 1255, 1257 and 1258, 1260 and 1261, 1263 and 1264, 1266 and1267, 1269 and 1270, 1272 and 1273, 1275 and 1276, 1278 and 1279, 1281and 1282, 1284 and 1285, 1287 and 1288, 1290 and 1291, 1293 and 1294,1296 and 1297, 1299 and 1300, 1302 and 1303, 1305 and 1306, 1308 and1309, 1311 and 1312, 1314 and 1315, 1317 and 1318, 1320 and 1321, 1323and 1324, 1326 and 1327, 1329 and 1330, 1332 and 1333, 1335 and 1336,1338 and 1339, 1341 and 1342, 1344 and 1345, 1347 and 1348, 1350 and1351, 1353 and 1354, 1356 and 1357, 1359 and 1360, 1362 and 1363, 1365and 1366, 1368 and 1369, 1371 and 1372, 1374 and 1375, 1377 and 1378,1380 and 1381, 1383 and 1384, 1386 and 1387, 1389 and 1390, 1392 and1393, 1395 and 1396, 1398 and 1399, 1401 and 1402, 1404 and 1405, 1407and 1408, 1410 and 1411, 1413 and 1414, 1416 and 1417, 1419 and 1420,1422 and 1423, 1425 and 1426, 1428 and 1429, 1431 and 1432, 1434 and1435, 1437 and 1438, 1440 and 1441, 1443 and 1444, 1446 and 1447, 1449and 1450, 1452 and 1453, 1455 and 1456, 1458 and 1459, 1461 and 1462,1464 and 1465, 1467 and 1468, 1470 and 1471, 1473 and 1474, 1476 and1477, 1479 and 1480, 1482 and 1483, 1485 and 1486, 1488 and 1489, 1491and 1492, 1494 and 1495, 1497 and 1498, 1500 and 1501, 1503 and 1504,1506 and 1507, 1509 and 1510, 1512 and 1513, 1515 and 1516, 1518 and1519, 1521 and 1522, 1524 and 1525, 1527 and 1528, 1530 and 1531, 1533and 1534, 1536 and 1537, 1539 and 1540, 1542 and 1543, 1545 and 1546,1548 and 1549, 1551 and 1552, 1554 and 1555, 1557 and 1558, 1560 and1561, 1563 and 1564, 1566 and 1567, 1569 and 1570, 1572 and 1573, 1575and 1576, 1578 and 1579, 1581 and 1582, 1584 and 15685, 1587 and 1588,1590 and 1591, 1593 and 1594, 1596 and 1597, 1599 and 1600, 1602 and1603, 1605 and 1606, 1608 and 1609, 1611 and 1612, 1614 and 1615, 1617and 1618, 1620 and 1621, 1623 and 1624, 1626 and 1627, 1629 and 1630,1632 and 1633, 1635 and 1636, 1638 and 1639, 1641 and 1642, 1644 and1645, 1647 and 1648, 1650 and 1651, 1653 and 1654, 1656 and 1657, 1659and 1660, 1662 and 1663, 1665 and 1666, 1668 and 1669, 1671 and 1672,1674 and 1675, 1677 and 1678, 1680 and 1681, 1683 and 1684, 1686 and1687, 1689 and 1690, 1692 and 1693, 1695 and 1696, 1698 and 1699, 1701and 1702, 1704 and 1705, 1707 and 1708, 1710 and 1711, 1713 and 1714,1716 and 1717, 1719 and 1720, 1722 and 1723, 1725 and 1726, 1728 and1729, 1731 and 1732, 1734 and 1735, 1737 and 1738, 1740 and 1741, 1743and 1744, 1746 and 1747, 1749 and 1750, 1752 and 1753, 1755 and 1756,1758 and 1759, 1761 and 1762, 1764 and 1765, 1767 and 1768, 1770 and1771, 1773 and 1774, 1776 and 1777, 1779 and 1780, 1782 and 1783, 1785and 1786, 1788 and 1789, 1791 and 1792, 1794 and 1795, 1797 and 1798,1800 and 1801, 1803 and 1804, 1806 and 1807, 1809 and 1810, 1812 and1813, 1815 and 1816, 1818 and 1819, 1821 and 1822, 1824 and 1825, 1827and 1828, 1830 and 1831, 1833 and 1834, 1836 and 1837, 1839 and 1840,1842 and 1843, 1845 and 1846, 1848 and 1849, 1851 and 1852, 1854 and1855, 1857 and 1858, 1860 and 1861, 1863 and 1864, 1866 and 1867, 1869and 1870, 1872 and 1873, 1875 and 1876, 1878 and 1879, 1881 and 1882,1884 and 1885, 1887 and 1888, 1890 and 1891, 1893 and 1894, 1896 and1897, 1899 and 1900, 1902 and 1903, 1905 and 1906, 1908 and 1909, 1911and 1912, 1914 and 1915, 1917 and 1918, 1920 and 1921, 1923 and 1924,1926 and 1927, 1929 and 1930, 1932 and 1933, 1925 and 1936, 1938 and1939, 1941 and 1942, 1944 and 1945, 1947 and 1948, 1950 and 1951, 1953and 1954, 1956 and 157, 1959 and 1960, 1962 and 1963, 1965 and 1966,1968 and 1969, 1971 and 1972, 1974 and 175, 1977 and 1978, 1980 and1981, 1983 and 1984, 1986 and 1987, 1989 and 1999, 1992 and 1993, 1995and 1996, 1998 and 1999, 2001 and 2002, 2004 and 2005, 2007 and 2008,2010 and 2011, 2013 and 2014, 2016 and 2017, 2019 and 2020, 2022 and2023, 2025 and 2026, 2028 and 2029, 2031 and 2032, 2034 and 2035, 2037and 2038, 2040 and 2041, 2043 and 2044, 2046 and 2047, 2049 and 2050,2052 and 2053, 2055 and 2056, or 2058 and 2059 of an NS3/4A nucleic acidsequence such as SEQ ID NO: 1, or between any of the codons of a nucleicacid sequence encoding an NS3/4A variant (e.g., SEQ ID NO: 35). Forexample, in some embodiments, a nucleic acid encoding a TCE or a TCE anda linker(s) and/or an adjuvant sequence is inserted between nucleotides1370 and 1548 of SEQ ID NO:35, or in an analogous position in any NS3/4Anucleic acid. Embodiments also relate to polypeptides encoded by saidnucleic acids.

In some embodiments, the nucleic acid sequences encoding the TCE or TCEand linker and/or adjuvant sequence portion of the chimeric NS3/4Apolypeptide can be juxtaposed to the 5′ end of the NS3/4A sequences, andencoding a chimeric NS3/4A polypeptide with a TCE or TCE and linker(s)and/or adjuvant sequence on the N-terminal end of the NS3/4Apolypeptide. In some embodiments, the nucleic acid sequences encodingthe TCE or TCE and linker(s) and/or adjuvant sequence polypeptide can beflanking (e.g., juxtaposed to) the 3′ end of the NS3/4A sequences andencode a chimeric NS3/4A polypeptides with a TCE or TCE and linker(s)and/or adjuvant sequence on the C-terminal end of the NS3/4Apolypeptide. In embodiments in which the chimeric NS3/4A polypeptidecomprises more than one TCE or TCE and linker(s) and/or adjuvantsequence, the nucleic acids encoding the TCEs can be located differentpositions relative to the nucleic acids encoding the NS3/4A sequences(i.e., 5′, within, or 3′) and relative to each other. Optionally, NS3/4Avariants include a substitution of at least one amino acid with anyother amino acid in one or more of the domains of a different NS3/NS4Asequences. Embodiments also relate to polypeptides encoded by saidnucleic acid sequences.

The skilled artisan will readily appreciate that a variety of techniquescan be used to generate variants, such as the generation of insertionsof desired sequences (e.g., TCEs and linkers) within NS3/4A nucleic acidand polypeptide sequences described herein. For example, overlapping PCRcan be used to generate desired substitutions or insertions (e.g., anucleic acid encoding a TCE, and/or linker sequences) within the NS3/4Asequences, or at the 3′ or 5′ ends of the NS3/4A sequences. (See, e.g.,Ho et al. (1989), Gene 77(1):51-9). Several commercially available kitsare also available to facilitate site-directed mutagenesis, tofacilitate the generation of NS3/4A variants, such as the recombinantnucleic acids and encoded polypeptides disclosed herein. An exemplarycommercially available kit useful for generating chimeric NS3/4Apolypeptides and chimeric NS3/4A polypeptide variants is theQUICKCHANGE® site directed mutagenesis kit (Stratagene, La Jolla,Calif.).

In preferred embodiments, the catalytic activity (e.g., the protease orhelicase activity) of a chimeric NS3/4A or chimeric NS3/4A variant maybe enhanced or unchanged, relative to the native polypeptide, or may bediminished by less than 50%, and preferably less than 20% relative tothe native polypeptide. In some embodiments the protease activity of anNS3/4A chimeric polypeptide or chimeric polypeptide variant isdiminished by less than 30%, 25%, 20%, 19%, 18%, 17%, 16%, 15%, 10%, 9%,8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5%, relative to the nativepolypeptide. In some embodiments the protease activity of an NS3/4Avariant may be enhanced by at least 30%, 25%, 20%, 19%, 18%, 17%, 16%,15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5%, relative to thenative polypeptide. Exemplary NS3/4A variants with altered proteaseactivity are discussed in further detail herein.

In preferred embodiments, the NS3/4A chimeric polypeptide retainsprotease activity. Accordingly, in some embodiments, the nucleic acidsencoding the chimeric NS3/4A polypeptide encode or the chimeric NS3/4Apolypeptides comprise the native amino acid sequence at the followingpositions of the NS3/4A sequence: Leu44, Ile48, Trp53, His57, Asp81,Trp85, Ala91, Leu94, Cys97, Cys99, Leu106, Thr108, Arg123, Gly124,Leu126, Ser139, Gly140, Leu143, Leu144, Cys145, His149, Ile153, Phe169,and Leu175. That is, the aforementioned residues are unchanged in someembodiments or, in some embodiments, the nucleic acids encoding TCEs orTCEs and linkers and/or adjuvant sequence are not substituted for,inserted within, or inserted at positions adjacent to nucleic acidsequences encoding the following amino acids of NS3/4A sequences: Leu44,Ile48, Trp53, His57, Asp81, Trp85, Ala91, Leu94, Cys97, Cys99, Leu106,Thr108, Arg123, Gly124, Leu126, Ser139, Gly140, Leu143, Leu144, Cys145,His149, Ile153, Phe169, and Leu175.

In some embodiments, the chimeric NS3/4A variants exhibit enhancedprotease activity. Embodiments disclosed herein provide NS3/4A chimericpolypeptides including one or more of the following amino acidsubstitutions in the NS3/4A sequence: Tyr6Ala, Arg11Ala, Leu13Ala,Leu14Ala, Glu30Ala, Cys52Ala, Gly58Ala, Ala59Gly, Ile64Ala, Ile64Ala,Gln73Ala, Thr76Ala, Pro86Ala, Ala111Gly, Gly 122Ala, Tyr 134Ala, Lys136Ala, Gly 141Ala, Val158Ala, Arg161Ala, Ala166Gly, or Thr177Ala. Thatis, in some embodiments one or more of the following amino acidsubstitutions are included: Tyr6Ala, Arg11Ala, Leu13Ala, Leu14Ala,Glu30Ala, Cys52Ala, Gly58Ala, Ala59Gly, Ile64Ala, Ile64Ala, Gln73Ala,Thr76Ala, Pro86Ala, Ala111Gly, Gly 122Ala, Tyr 134Ala, Lys 136Ala, Gly141Ala, Val158Ala, Arg161Ala, Ala166Gly, or Thr177Ala.

In some embodiments, NS3/4A variant sequences used in the embodimentsdisclosed herein lack a proteolytic cleavage site, such as SEQ. ID.NOs.: 14 and 16-26. In some embodiments, fragments of the NS3/4A variantsequences containing any number of consecutive amino acids between atleast 3-300 amino acids (e.g., 3, 4, 6, 8, 10, 12, 15, 20, 25, 30, 35,40, 45, 50, 75, 100, 150, 200, 250, or 300 consecutive amino acids) ofany one of SEQ. ID. NOs.: 14 and 16-26 are used in the embodimentsdisclosed herein. Other exemplary NS3/4A variants with altered proteaseactivity may generally be identified by modifying one or more of theabove nucleic acid or polypeptide sequences and evaluating the proteaseactivity of the variant, as discussed in further detail in Example 1.

In some embodiments, the helicase activity of a NS3/4A variant isdiminished by less than 30%, 25%, 20%, 19%, 18%, 17%, 16%, 15%, 10%, 9%,8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5%, relative to the nativepolypeptide. In some embodiments the helicase activity of an NS3/4Avariant may be enhanced by at least 30%, 25%, 20%, 19%, 18%, 17%, 16%,15%, 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5%, relative to thenative polypeptide. Such variants may generally be identified bymodifying one of the above polypeptide sequences and evaluating thehelicase activity as described herein

Guidance in determining the identity of amino acids that may affect NS3helicase activity can be found by comparing the sequence of the NS3helicase domain with that of homologous known protein molecules andminimizing the number of amino acid sequence changes made in regions ofhigh homology. An exemplary assay for testing variants for helicaseactivity is discussed in Artsaenko O, et al., (2003) J Gen Virol. 200384(Pt 9):2323-32, and Zhang et al., (2005) J. Virol. 79(14):8687-97; andKyono et al., (2004) J Biochem (Tokyo) 135(2):245-52.

Optionally, chimeric NS3/4A variants can encode or comprise amino acidsubstitutions, wherein one amino acid is substituted with another aminoacid having similar structural and/or chemical properties (e.g.,conservative amino acid replacements). A list of conservative amino acidsubstitutions can be found in Table 1.

TABLE 1 Original Exemplary Preferred Residue Substitutions SubstitutionsAla (A) val; leu; ile val Arg (R) lys; gln; asn lys Asn (N) gln; his;lys; arg gln Asp (D) glu glu Cys (C) ser ser Gln (Q) asn asn Glu (E) aspasp Gly (G) pro; ala ala His (H) asn; gln; lys; arg arg Ile (I) leu;val; met; ala; phe; leu norleucine Leu (L) norleucine; ile; val; ilemet; ala; phe Lys (K) arg; gln; asn arg Met (M) leu; phe; ile leu Phe(F) leu; val; ile; ala; tyr leu Pro (P) ala ala Ser (S) thr thr Thr (T)ser ser Trp (W) tyr; phe tyr Tyr (Y) trp; phe; thr; ser phe Val (V) ile;leu; met; phe; leu ala; norleucine

In some embodiments, variant NS3/4A sequences are engineered oroptimized for codons most frequently used in humans. The nucleic acidsequence of an exemplary codon-optimized NS3/4A nucleic acid sequence(coNS3/4A) is provided in SEQ. ID. NO.:35. The peptide encoded by saidnucleic acid sequence is provided in SEQ. ID. NO.: 36. The skilledartisan will appreciate, however, that any HCV NS3/4A sequencesdisclosed herein or discovered in the future can be used to generatecodon-optimized variants and that all codon-optimized variants arewithin the scope of the present invention.

The nucleic acid and corresponding NS3/4A peptide (SEQ ID NOs: 35 and36) do not correspond to any known HCV sequence or genome. Thecodon-optimized NS3/4A encoding nucleic acid was found to be only 79%homologous, within the region of nucleotide positions 3417-5475, toHCV-1 and contained a total of 433 different nucleotides. The NS3/4Apeptide encoded by the codon-optimized nucleic acid sequence is only 98%homologous to HCV-1 and contained a total of 15 different amino acids.As demonstrated in Example 2, below, the codon optimized nucleic acidwas found to generate a higher expression level of NS3 and was found tobe more immunogenic, with respect to both humoral and cellularresponses, as compared to the native NS3/4A gene from which it wasderived. Accordingly, in preferred embodiments, the NS3/4A nucleic acidsequences encoding, or the encoded polypeptide sequences of the NS3/4Achimeric polypeptides comprise codon-optimized nucleic acid andpolypeptide sequences of native HCV sequences. For example, in someembodiments, the NS3/4A nucleic acid sequences or encoded polypeptidesequences of an NS3/4A chimeric polypeptides comprises SEQ ID NO: 35 orSEQ ID NO: 36, or fragments thereof, or variants thereof and TCEs and/orlinker sequences.

Example 2

The sequence of the unique NS3/4A gene described in Example 1 (SEQ. ID.NO.: 1) was analyzed for codon usage with respect to the most commonlyused codons in human cells. A total of 435 nucleotides were replaced tooptimize codon usage for human cells. The sequence was sent to RetrogenInc. (6645 Nancy Ridge Drive, San Diego, Calif. 92121) and they wereprovided with instructions to generate a full-length synthetic codonoptimized NS3/4A gene. The codon optimized NS3/4A gene had a sequencehomology of 79% within the region between nucleotide positions 3417-5475of the HCV-1 reference strain. A total of 433 nucleotides differed. Onan amino acid level, the homology with the HCV-1 strain was 98% and atotal of 15 amino acids differed.

The full length codon optimized 2.1 kb DNA fragment of the HCVcorresponding to the amino acids 1007 to 1711 encompassing the NS3 andNS4A NS3/4A gene fragment was amplified by the polymerase chain reaction(PCR) using high fidelity polymerase (Expand High Fidelity PCR,Boehringer-Mannheim, Mannheim, Germany). The amplicon was then insertedinto a Bam HI and Xba I digested pVAX vector (Invitrogen, San Diego),which generated the MSLF1-pVAX (coNS3/4A-pVAX) plasmid. All expressionconstructs were sequenced. Plasmids were grown in competent BL21 E.Coli. The plasmid DNA used for in vivo injection was purified usingQiagen DNA purification columns, according to the manufacturersinstructions (Qiagen GmbH, Hilden, FRG). The concentration of theresulting plasmid DNA was determined spectrophotometrically (Dynaquant,Pharmacia Biotech, Uppsala, Sweden) and the purified DNA was dissolvedin sterile phosphate buffer saline (PBS) at concentrations of 1 mg/ml.

The expression of NS3 and NS3/4A proteins from the wtNS3/4A (wild-typeNS3/4A) and coNS3/4A plasmids, were analyzed by an in vitrotranscription and translation assay. The assay showed that the proteinscould be correctly translated from the plasmids and that the coNS3/4Aplasmid gave detectable NS3 and NS3/4A bands at a higher plasmiddilution as compared to the wtNS3/4A plasmid. This result providedstrong evidence that the in vitro translation from the coNS3/4A plasmidis more effective than wtNS3/4A. To compare the expression levels moreprecisely, HepG2 cells were transiently transfected with the wtNS3/4Aand the coNS3/4A plasmids. These experiments revealed that the coNS3/4Aplasmid generated 11-fold higher expression levels of the NS3 proteinwhen compared to the wtNS3/4A plasmid, as determined by densitometry anda standard curve of recombinant NS3. Since the wtNS3/4A and the coNS3/4Aplasmids are identical in size it is unlikely that there would be anymajor differences in transfections efficiencies between the plasmids.Staining of coNS3/4A plasmid transfected, and SFV infected, BHK cellsrevealed a similar perinuclear and cytoplasmic distribution of the NS3as previously observed, confirming an unchanged subcellularlocalization.

TABLE 2 describes the sequence of the proteolytic cleavage site ofNS3/4A, referred to as the breakpoint between NS3 and NS4A. Thiswild-type breakpoint sequence was mutated in many different ways so asto generate several different NS3/4A breakpoint mutants. TABLE 2 alsoidentifies these mutant breakpoint sequences. The fragments listed inTABLE 2 are preferred immunogens that can be incorporated with orwithout an adjuvant (e.g., ribavirin) into a composition foradministration to an animal so as to induce an immune response in saidanimal to HCV.

TABLE 2 Deduced amino acid SEQ Plasmid  sequence ID NS3/4A-pVAXTKYMTCMSADLEVVTSTWVLVGGVL 14 NS3/4A-TGT-pVAX TKYMTCMSADLEVVTGTWVLVGGVL16 NS3/4A-RGT-pVAX TKYMTCMSADLEVVRGTWVLVGGVL 17 NS3/4A-TPT-pVAXTKYMTCMSADLEVVTPTWVLVGGVL 18 NS3/4A-RPT-pVAX TKYMTCMSADLEVVRPTWVLVGGVL19 NS3/4A-RPA-pVAX TKYMTCMSADLEVVRPAWVLVGGVL 20 NS3/4A-CST-pVAXTKYMTCMSADLEVVCSTWVLVGGVL 21 NS3/4A-CCST-pVAX TKYMTCMSADLEVCCSTWVLVGGVL22 NS3/4A-SSST-pVAX TKYMTCMSADLEVSSSTWVLVGGVL 23 NS3/4A-SSSSCST-pVAXTKYMTCMSADSSSSCSTWVLVGGVL 24 NS3A/4A-VVVVTST-pVAXTKYMTCMSADVVVVTSTWVLVGGVL 25 NS5-pVAX ASEDVVCCSMSYTWTG 27 NS5A/B-pVAXSSEDVVCCSMWVLVGGVL 26

-   -   *The wild type sequence for the NS3/4A fragment is NS3/4A-pVAX.        The NS3/4A breakpoint is identified by underline, wherein the P1        position corresponds to the first Thr (T) and the P1′ position        corresponds to the next following amino acid the NS3/4A-pVAX        sequence. In the wild type NS3/4A sequence the NS3 protease        cleaves between the P1 and P1′ positions.

To change the proteolytic cleavage site between NS3 and NS4A, theNS3/4A-pVAX plasmid was mutagenized using the QUICKCHANGE™ mutagenesiskit (Stratagene), following the manufacturer's recommendations. Togenerate the “TPT” mutation, for example, the plasmid was amplifiedusing the primers 5′-CTGGAGGTCGTCACGCCTACCTGGGTGCTCGTT-3′ (SEQ. ID. NO.:31) and 5′-ACCGAGCACCCAGGTAGGCGTGACGACCTCCAG-3′ (SEQ. ID. NO.: 32)resulting in NS3/4A-TPT-pVAX. To generate the “RGT” mutation, forexample, the plasmid was amplified using the primers5′-CTGGAGGTCGTCCGCGGTACCTGGGTGCTCGTT-3′ (SEQ. ID. NO.: 33) and5′-ACCGAGCACCCAGGTACC-GCGGACGACCTCCAG-3′ (SEQ. ID. NO.: 34) resulting inNS3/4A-RGT-pVAX. All mutagenized constructs were sequenced to verifythat the mutations had been correctly made. Plasmids were grown incompetent BL21 E. coli.

On an amino acid level, the homology with the HCV-1 strain was 98% and atotal of 15 amino acids differed. The nucleic acid sequence of thecodon-optimized NS3/4a is provided in SEQ ID NO: 35, whereas the peptideencoded by said nucleic acid sequence is provided in SEQ ID NO:36. Thefull length codon optimized 2.1 kb DNA fragment of the HCV correspondingto the amino acids 1007 to 1711 encompassing the NS3 and NS4A NS3/4Agene fragment was amplified by the polymerase chain reaction (PCR) usinghigh fidelity polymerase (Expand High Fidelity PCR, Boehringer-Mannheim,Mannheim, Germany). The amplicon was then inserted into a Bam HI and XbaI digested pVAX vector (Invitrogen, San Diego), which generated theMSLF1-pVAX (coNS3/4A-pVAX) plasmid. All expression constructs weresequenced. Plasmids were grown in competent BL21 E. Coli. The plasmidDNA used for in vivo injection was purified using Qiagen DNApurification columns, according to the manufacturers instructions(Qiagen GmbH, Hilden, FRG). The concentration of the resulting plasmidDNA was determined spectrophotometrically (Dynaquant, Pharmacia Biotech,Uppsala, Sweden) and the purified DNA was dissolved in sterile phosphatebuffer saline (PBS) at concentrations of 1 mg/ml.

The expression of NS3 and NS3/4A proteins from the wtNS3/4A (wild-typeNS3/4A) and coNS3/4A plasmids, were analyzed by an in vitrotranscription and translation assay. The assay showed that the proteinscould be correctly translated from the plasmids and that the coNS3/4Aplasmid gave detectable NS3 and NS3/4A bands at a higher plasmiddilution as compared to the wtNS3/4A plasmid. This result providedstrong evidence that the in vitro translation from the coNS3/4A plasmidis more effective than wtNS3/4A. To compare the expression levels moreprecisely, HepG2 cells were transiently transfected with the wtNS3/4Aand the coNS3/4A plasmids. These experiments revealed that the coNS3/4Aplasmid generated 11-fold higher expression levels of the NS3 proteinwhen compared to the wtNS3/4A plasmid, as determined by densitometry anda standard curve of recombinant NS3. Since the wtNS3/4A and the coNS3/4Aplasmids are identical in size it is unlikely that there would be anymajor differences in transfections efficiencies between the plasmids.Staining of coNS3/4A plasmid transfected, and SFV infected, BHK cellsrevealed a similar perinuclear and cytoplasmic distribution of the NS3as previously observed, confirming an unchanged subcellularlocalization.

Several nucleic acid embodiments include nucleotides encoding the HCVpeptides described herein (SEQ. ID. NOs.: 2-11 or SEQ. ID. NO.: 36) or afragment thereof (e.g., SEQ. ID. NOs.: 14 and 15) containing any numberof consecutive amino acids between at least 3-50 (e.g., 3, 4, 6, 8, 10,12, 15, 20, 25, 30, 35, 40, 45, or 50 amino acids in length). Someembodiments for example, include genomic DNA, RNA, and cDNA encodingthese HCV peptides. The HCV nucleotide embodiments not only include theDNA sequences shown in the sequence listing (e.g., SEQ. ID. NO.: 1 orSEQ. ID. NO.: 35) but also include nucleotide sequences encoding theamino acid sequences shown in the sequence listing (e.g., SEQ. ID. NOs.:2-11 or SEQ. ID. NO.: 36) and any nucleotide sequence that hybridizes tothe DNA sequences shown in the sequence listing under stringentconditions (e.g., hybridization to filter-bound DNA in 0.5 M NaHPO₄,7.0% sodium dodecyl sulfate (SDS), 1 mM EDTA at 50° C.) and washing in0.2×SSC/0.2% SDS at 50° C. and any nucleotide sequence that hybridizesto the DNA sequences that encode an amino acid sequence provided in thesequence listing (SEQ. ID. NOs.: 2-11 or SEQ. ID. NO.: 36) under lessstringent conditions (e.g., hybridization in 0.5 M NaHPO₄, 7.0% sodiumdodecyl sulfate (SDS), 1 mM EDTA at 37° C. and washing in 0.2×SSC/0.2%SDS at 37° C.).

The nucleic acid embodiments of the invention also include fragments,modifications, derivatives, and variants of the sequences describedabove. Desired embodiments, for example, include nucleic acids having atleast 25 consecutive bases of one of the novel HCV sequences or asequence complementary thereto and preferred fragments include at least25 consecutive bases of a nucleic acid encoding the NS3/4A molecule ofSEQ. ID. NO.: 2 or SEQ. ID. NO.: 36 or a mutant NS3/4A molecule of SEQ.ID. NOs.: 3-13 or a sequence complementary thereto.

In this regard, the nucleic acid embodiments described herein can haveany number of consecutive nucleotides between about 12 to approximately2112 consecutive nucleotides of SEQ. ID. NO.: 1 or SEQ. ID. NO.: 35.Some DNA fragments, for example, include nucleic acids having at least12-15, 15-20, 20-30, 30-50, 50-100, 100-200, 200-500, 500-1000,1000-1500, 1500-2079, or 1500-2112 consecutive nucleotides of SEQ. ID.NO.: 1 or SEQ. ID. NO.: 35 or a complement thereof. These nucleic acidembodiments can also be altered by substitution, addition, or deletionso long as the alteration does not significantly affect the structure orfunction (e.g., ability to serve as an immunogen) of the HCV nucleicacid. Due to the degeneracy of nucleotide coding sequences, for example,other DNA sequences that encode substantially the same HCV amino acidsequence as depicted in SEQ. ID. NOs.: 2-13 or SEQ. ID. NO.: 36 can beused in some embodiments. These include, but are not limited to, nucleicacid sequences encoding all or portions of HCV peptides (SEQ. ID. NOs.:2-13) or nucleic acids that complement all or part of this sequence thathave been altered by the substitution of different codons that encode afunctionally equivalent amino acid residue within the sequence, thusproducing a silent change, or a functionally non-equivalent amino acidresidue within the sequence, thus producing a detectable change.Accordingly, the nucleic acid embodiments of the invention are said tobe comprising, consisting of, or consisting essentially of nucleic acidsencoding any one of SEQ. ID. NOs.: 2-27 or SEQ. ID. NO.: 36 in light ofthe modifications above.

In some embodiments, the HCV NS3/4A sequences comprise, consistessentially of, or consist of NS3 and or NS4A sequences that encodefragments, or functional fragments of the full-length NS3/4Apolypeptide. Such fragments may be truncated at the N-terminus orC-terminus, or may lack internal residues, for example, when comparedwith a full length native protein. In preferred embodiments, NS3/4Afragments lack amino acid residues that are not essential for thecatalytic activity of the NS3 polypeptide. For example, in someembodiments the NS3/4A sequences can comprise, consist, or consistessentially of fragments of any of SEQ ID NOs: 1, 35, and 572-808encoding any number of consecutive amino acids (e.g., 3, 4, 6, 8, 10,12, 15, 20, 25, 30, 35, 40, 45, 50, 75, 100, 150, 200, 250, or 300consecutive amino acids). The section below describes several antigensthat can be used in the compositions and methods described herein.

Epitopes

The chimeric NS3/4A nucleic acids and polypeptides disclosed hereininclude sequences comprising antigens, such as TCEs, positioned atnon-naturally occurring locations, either within and/or flanking (e.g.,juxtaposed to) NS3/4A sequences. As used herein, the term epitope refersto a set of amino acid residues that are involved in recognition by aparticular immunoglobulin (i.e., a B cell epitope or “BCE”) or in thecontext of TCE, those residues necessary for recognition by T cellreceptor proteins and/or Major Histocompatibility Complex (MHC)receptors. In an immune system setting, in vivo or in vitro, an epitopeis the collective features of a molecule, such as primary, secondary,and tertiary peptide structure, and charge, that together form a siterecognized by an immunoglobulin, T cell receptor, or HLA molecule. TCEsare recognized by either CD4+ T cells, or helper T lymphocytes (“HTLs”)or CD8+ T cells, or cytotoxic T lymphocytes (“CTLs”).

TCEs generally comprise a chain of at least four amino acid residues,preferably at least six, more preferably eight to ten, sometimes elevento fourteen residues, and usually fewer than about thirty residues, moreusually fewer than about twenty-five, and preferably fewer than fifteen,e.g., eight to fourteen amino acid residues derived from selectedepitopic regions of the target antigen(s). It is to be appreciated,however, that TCE nucleic acids, or TCE amino acid sequences can referto nucleic acids encoding or protein or peptide molecules, larger thanand comprising an epitope of the invention are still within the scope ofthe invention. For example, nucleic acid and polypeptide sequences offull length proteins that contain at least one TCE, that are capable ofproducing an immune response are contemplated for use in someembodiments.

In some aspects, the TCE are nucleic acids encoding peptides whereinsaid nucleic acids are, are at least, are at least about, are less than,or are less than about 3 nucleotides, 4 nucleotides, 5 nucleotides, 6nucleotides, 7 nucleotides, 8 nucleotides, 9 nucleotides, 10nucleotides, 11 nucleotides, 12 nucleotides, 13 nucleotides, 14nucleotides, 15 nucleotides, 16 nucleotides, 17 nucleotides, 18nucleotides, 19 nucleotides, 20 nucleotides, 21 nucleotides, 22nucleotides, 23 nucleotides, 24 nucleotides, 25 nucleotides, 26nucleotides, 27 nucleotides, 28 nucleotides, 29 nucleotides, 30nucleotides, 31 nucleotides, 32 nucleotides, 33 nucleotides, 34nucleotides, 35 nucleotides, 36 nucleotides, 37 nucleotides, 38nucleotides, 39 nucleotides, 40 nucleotides, 41 nucleotides, 42nucleotides, 43 nucleotides, 44 nucleotides, 45 nucleotides, 46nucleotides, 47 nucleotides, 48 nucleotides, 49 nucleotides, 50nucleotides, 55 nucleotides, 60 nucleotides, 65 nucleotides, 70nucleotides, 75 nucleotides, 80 nucleotides, 85 nucleotides, 90nucleotides, 95 nucleotides, 100 nucleotides, 110 nucleotides, 120nucleotides, 130 nucleotides, 140 nucleotides, 150 nucleotides, 160nucleotides, 170 nucleotides, 180 nucleotides, 190 nucleotides, 200nucleotides, 250 nucleotides, 300 nucleotides, 350 nucleotides, 400nucleotides, 450 nucleotides, 500 nucleotides, 550 nucleotides, 600nucleotides, 650 nucleotides, 700 nucleotides, 750 nucleotides, 800nucleotides, 850 nucleotides, 900 nucleotides, 950 nucleotides, 1000nucleotides, 1100 nucleotides, 1200 nucleotides, 1300 nucleotides, 1400nucleotides, 1500 nucleotides, 1600 nucleotides, 1700 nucleotides, 1800nucleotides, 1900 nucleotides, 2000 nucleotides, 2500 nucleotides, 3000nucleotides, 3500 nucleotides, 4000 nucleotides, 4500 nucleotides, 5000nucleotides, 6000 nucleotides, 7000 nucleotides, 8000 nucleotides, 9000nucleotides, 10,000 nucleotides in length

In some aspects, the TCE are peptides or peptide fragments that are, areat least, are at least about, are less than, or are less than about 3amino acids, 4 amino acids, 5 amino acids, 6 amino acids, 7 amino acids,8 amino acids, 9 amino acids, 10 amino acids, 11 amino acids, 12 aminoacids, 13 amino acids, 14 amino acids, 15 amino acids, 16 amino acids,17 amino acids, 18 amino acids, 19 amino acids, 20 amino acids, 21 aminoacids, 22 amino acids, 23 amino acids, 24 amino acids, 25 amino acids,26 amino acids, 27 amino acids, 28 amino acids, 29 amino acids, 30 aminoacids, 31 amino acids, 32 amino acids, 33 amino acids, 34 amino acids,35 amino acids, 36 amino acids, 37 amino acids, 38 amino acids, 39 aminoacids, 40 amino acids, 41 amino acids, 42 amino acids, 43 amino acids,44 amino acids, 45 amino acids, 46 amino acids, 47 amino acids, 48 aminoacids, 49 amino acids, 50 amino acids, 55 amino acids, 60 amino acids,65 amino acids, 70 amino acids, 75 amino acids, 80 amino acids, 85 aminoacids, 90 amino acids, 95 amino acids, 100 amino acids, 110 amino acids,120 amino acids, 130 amino acids, 140 amino acids, 150 amino acids, 160amino acids, 170 amino acids, 180 amino acids, 190 amino acids, 200amino acids, 250 amino acids, 300 amino acids, 350 amino acids, 400amino acids, 450 amino acids, 500 amino acids, 550 amino acids, 600amino acids, 650 amino acids, 700 amino acids, 750 amino acids, 800amino acids, 850 amino acids, 900 amino acids, 950 amino acids, 1000amino acids, 1100 amino acids, 1200 amino acids, 1300 amino acids, 1400amino acids, 1500 amino acids, 1600 amino acids, 1700 amino acids, 1800amino acids, 1900 amino acids, 2000 amino acids, 2500 amino acids, 3000amino acids, 3500 amino acids, 4000 amino acids, 4500 amino acids, 5000amino acids, 6000 amino acids, 7000 amino acids, 8000 amino acids, 9000amino acids, 10,000 amino acids in length.

Further, it will be appreciated that the term “TCE” includes sequencesthat comprise one, two, or multiple TCEs. For example, a TCE may referto a recombinant string of CTL and/or HTL epitopes. In some embodiments,the NS3/4A chimeric molecules disclosed herein include epitope stringsto generate a CTL response against any chosen antigen/target thatcontains such epitopes. Optionally, HTL epitopes which are active inindividuals of different HLA types, for example HTLs from tetanus(against which most individuals will already be primed) are present inthe embodiments disclosed herein. Further, in some embodiments, inaddition to a TCE, it may also be useful to include B cell epitopes forstimulating B cell responses and antibody production. Optionally,multiple epitope (e.g. multiple TCE and/or multiple TCE and BCE)conjugates can be engineered to be linked by a linker molecule. Linkerscan comprise relatively neutral amino acid sequences or amino acidmimetics, such as, e.g., Ala, Gly, or other neutral linkers of nonpolaramino acids or neutral polar amino acids. In certain preferredembodiments herein the neutral linker is Ala. It will be understood thatthe optionally present linker need not be comprised of the same residuesand thus may be a hetero- or homo-oligomer. Preferred exemplary linkersare homo-oligomers of Ala or Gly. When present, the linker will usuallybe at least one or two residues, more usually three to six residues.Adjuvant sequences such as nucleic acids encoding HIV TAT or fragmentsthereof (e.g., 3, 6, 9, 12, 15, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48,51, 54, 57, or 60 nucleotides in length) can be employed in someembodiments. Exemplary sequences can be found in WO05039631A1, whichdesignates the United states and was published in English, herebyexpressly incorporated by reference in its entirety. Optionally, linkersand/or adjuvant sequences flank, or are juxtaposed to TCE sequencesand/or NS3/4A sequences.

The compositions and methods disclosed herein relate to antigens againstwhich it is desired to generate an immune response. For example, thecompositions and methods disclosed herein are useful, for example, ingenerating or enhancing the immunogenicity of TCEs derived from agentsagainst which CD8⁺ T cell responses have been shown to play a protectiverole. As such, the compositions disclosed herein are useful in diseasesthat include but are not limited to infection and disease caused by theviruses including, but not limited to: influenza A and B viruses (FLU-A,FLU-B), human immunodeficiency type I and II viruses (HIV-I, HIV-II),Epstein-Barr virus (EBV), human T lymphotrophic (or T-cell leukemia)virus type I and type II (HTLV-I, HTLV-II), human papillomaviruses types1 to 18 (HPV-1 to HPV-18), rubella (RV), varicella-zoster (VZV),hepatitis B (HBV), hepatitis C(HCV), adenoviruses (AV), and herpessimplex virus (HSV), cytomegalovirus (CMV), poliovirus, respiratorysyncytial (RSV), rhinovirus, rabies, mumps, rotavirus or measlesviruses. Further, the compositions disclosed herein are useful indiseases caused by the bacteria Mycobacterium tuberculosis and Listeriasp.; and by the protozoan parasites Plasmodium, Toxoplasma andTrypanosoma and the like.

In a like manner, the compositions and methods described herein areapplicable to tumor-associated proteins (e.g., related to melanoma,breast cancer, colon cancer and the like), which could be sources forCTL epitopes. Such tumor proteins and/or peptides, include, but are notlimited to, products of the MAGE-1, -2 and -3 genes, products of thec-ErbB2 (HER-2/neu) proto-oncogene, tumor suppressor and regulatorygenes which could be either mutated or overexpressed such as p53, ras,myc, and RB1. Tissue specific proteins to target CTL responses to tumorssuch as prostatic specific antigen (PSA) and prostatic acid phosphatase(PAP) for prostate cancer, and tyrosinase for melanoma. In additionviral related proteins associated with cell transformation into tumorcells such as EBNA-1, HPV E6 and E7 are likewise applicable. A largenumber of peptides from some of the above proteins have been analyzedfor the presence of MHC-binding motifs and for their ability to bindwith high efficiency to purified MHC molecules and are the subject ofpending patent applications (U.S. patent application Ser. Nos.08/159,339 and 08/073,205, previously incorporated herein by reference)

The amino acid sequences of exemplary TCEs, including both HTL and CTLTCEs, are listed in Table 3. Nucleic acids encoding these sequences canbe readily generated by those of skill in the art.

TABLE 3 SEQ ID Epitope NO Source Sequence Source 222 EBV YLLEMLWRLU.S. 6,723,695* 223 EBV YFLEILWGL U.S. 6,723,695 224 EBV YLLEILWRLU.S. 6,723,695 225 EBV YLQQNWWTL U.S. 6,723,695 226 EBV LLLALLFWLU.S. 6,723,695 227 EBV LLVDLLWLL U.S. 6,723,695 228 EBV LLLIALWNLU.S. 6,723,695 229 EBV WLLLFLAIL U.S. 6,723,695 230 EBV TLLVDLLWLU.S. 6,723,695 231 EBV LLWLLLFLA U.S. 6,723,695 232 EBV ILLIIALYLU.S. 6,723,695 233 EBV VLFIFGCLL U.S. 6,723,695 234 EBV RLGATIWQLU.S. 6,723,695 235 EBV ILYFIAFAL U.S. 6,723,695 236 EBV SLVIVTTFVU.S. 6,723,695 237 EBV LMIIPLINV U.S. 6,723,695 238 EBV TLFIGSHVVU.S. 6,723,695 239 EBV LIPETVPYI U.S. 6,723,695 240 EBV QLTPHTKAVU.S. 6,723,695 241 EBV QNGALAINTF U.S. 6,703,024* 242 EBV LLDFVRFMGVU.S. 6,703,024 243 EBV QAKWRLQTL W0/95AU0000140 * 244 EBV RYSIFFDYWO/95AU0000140 245 EBV HLAAQGMAY WO/95AU0000140 246 EBV YPLHEQHGMWO/95AU0000140 247 EBV SVRDRLARL W0/95AU0000140 248 EBV AVLLHEESMWO/95AU0000140 249 EBV VSFIEFVGW, WO/95AU0000140 250 EBV FRKAQIQGLWO/95AU0000140 251 EBV PYLFWLAAI, WO/95AU0000140 252 EBV TVFYNIPPMPLW0/95AU0000140 253 EBV PGDQLPGFSDGRACPV WO/95AU0000140 254 EBVVEITPYKPTW W0/95AU0000140 255 EBV TYSAGIVQI U.S. 6,699,477* 256 HPVAQIFNKPYW, U.S. 6,911,207* 257 HPV AGVDNRECI U.S. 6,911,207 258 MAGE-1EADPTGHSY U.S. 6,419,931* (melanoma) 259 MAGE-2 KMVELVHFL U.S. 6,419,931260 MAGE-2 KMVELVHFLL U.S. 6,419,931 261 MAGE-3 LVFGIELMEVU.S. 6,419,931 262 MAGE-1 KVLEYVIKV U.S. 6,419,931 263 MAGE-1 KVADLVGFLLU.S. 6,419,931 264 MAGE-3 KVAEFVHFL U.S. 6,419,931 265 MAGE-1 CILESLFRAU.S. 6,419,931 266 MAGE-1 FLWGPRALA U.S. 6,419,931 267 MAGE-1 VMIAMEGGHAU.S. 6,419,931 268 MAGE-1 LVLGTLEEV U.S. 6,419,931 269 MAGE-1 ALREEEEGVU.S. 6,419,931 270 MAGE-1 ALAETSYVKV U.S. 6,419,931 271 MAGE-1 YVIKVSARVU.S. 6,419,931 272 MAGE-1 RALAETSYV U.S. 6,419,931 273 HIV nef84-94AVDLSHFLK U.S. 6,419,931 274 EBV NA4 416- IVTDFSVIK U.S. 6,419,931 424275 HBc18-27 FLPSDFFPSV U.S. 6,419,931 276 HIV RT ILKEPVHGVU.S. 6,419,931 277 HTLV-1, Tox 12- LFGYPVYV U.S. 6,419,931 19 278Influenza A, M1 GILGFVFTL U.S. 6,419,931 58-66 279 HCMV, gB 619-IAGNSAYEYV U.S. 6,419,931 628 280 Plasmodium GIEYLNKIQNSLSTEWSPCSVTU.S. 6,942,866* falciparum 281 Plasmodium YLDKVRATVGTEWTPCSVTU.S. 6,942,866 vivax 282 Plasmodium EFVKQISSQLTEEWSQCSVT U.S. 6,942,866yoelli 283 p53 264-272 LLGRNSFEV U.S. 6,419,931 284 HBVadr-ENV (SWLSLLVPFV U.S. 6,419,931 Ag335-343) 285 c-ErbB2 (HER- RFRELVSEFSRMARDPQU.S. 6,419,931 2/neu)(Breast cancer) 286 HIV nef73-82 QVPLRPMTYKU.S. 6,419,931 287 HIV-1 NL43 env RLRDLLLIVTR U.S. 6,419,931 gp41768-778288 HCV 141-151 STLPETTTVRR U.S. 6,419,931 289 Influenza virus SRYWAIRTRU.S. 6,419,931 NP 383-391 290 HIV gag p24 KRWIILGLNK U.S. 6,419,931265-274 291 P. falciparum KPKDELDY U.S. 6,419,931 circumsp. 368- 375 292P. falciparum KSKDLEDY U.S. 6,419,931 circumsp. 368- 375 293P. falciparum KPNDKSLY U.S. 6,419,931 liver Ag 1850- 1857 294 HIV-2TPYDINQML U.S. 6,419,931 295 P. falciparum KPIVQYDNF U.S. 6,419,931liverAg1786- 1794 296 B53 self peptide YPAEITLTW U.S. 6,419,931 297HIV gp41 586- YLKDQQLL U.S. 6,419,931 593 298 Influenza virus ELRSRYWAIU.S. 6,419,931 NP 380-388 299 EBV EBNA-3 FLRGRAYGI U.S. 6,419,931 300HIV gag261-269 GEIYKRWII U.S. 6,419,931 301 HIV gag331-339 DCKTILKALU.S. 6,419,931 302 HIV pol185-193 DPKVKQWPL U.S. 6,419,931 303HIV gp41 586- YLKDQQLYL U.S. 6,419,931 593 304 HIV gap p17.3 GGKKKYKLKU.S. 6,419,931 305 HBV POL LLAQFTSAI U.S. 6,419,931 306 HBV ENVLLVPFVQWFV U.S. 6,419,931 307 HBV ENV WLSLLVPFV U.S. 6,419,931 308HBV ENV FLLAQFTSA U.S. 6,419,931 309 HBV POL FLLSLGIHL U.S. 6,419,931310 HBV POL ALMPLYACI U.S. 6,419,931 311 HBV ENV ILLLCLIFLLU.S. 6,419,931 312 HBV POL KIJLYSHPI U.S. 6,419,931 313 HBV ENVVLLDYQGML U.S. 6,419,931 314 HBV ENV LLPIFFCLWV U.S. 6,419,931 315HBV ENV VLQAGFFLL U.S. 6,419,931 316 HBV POL YLHTLWKAGI U.S. 6,419,931317 HBV POL YLHTLWKAGV U.S. 6,419,931 318 HBV ENV PLLPIFFCLU.S. 6,419,931 319 HBV NUC ILSTLPETTV U.S. 6,419,931 320 HCV NS4LLFNILGGWV U.S. 6,419,931 321 HCV CORE LLALLSCLTV U.S. 6,419,931 322HCV NS4 YLVAYQATV U.S. 6,419,931 323 HCV NS1/ENV FLLLADARVU.S. 6,419,931 324 HCV NS4 ILAGYGAGV U.S. 6,419,931 325 HCV COREDLMGYIPLV U.S. 6,419,931 326 HCV CORE YLLPRRGPRL U.S. 6,419,931 327NS1/ENV2 ALSTGLIHL U.S. 6,419,931 328 HCV CORE LLALLSCLTI U.S. 6,419,931329 HCV NS5 RLIVFPDLGV U.S. 6,419,931 330 HCV NS5 RLHGLSAFSLU.S. 6,419,931 331 HCV NS4 ILGGWVAAQL U.S. 6,419,931 332 HCV ENV1SMVGNWAKV U.S. 6,419,931 333 HCV NS3 YLVTRHADV U.S. 6,419,931 334HCV NS4 VLAALAAYCL U.S. 6,419,931 335 HPV16 E7 LLMGTLGIV U.S. 6,419,931336 HPV16 E7 YMLDLQPET U.S. 6,419,931 337 HPV16 E6 FAFRDLCIVU.S. 6,419,931 338 HPV16 E7 TLGIVCPIC U.S. 6,419,931 339 HPV16 E7TLHEYMLDL U.S. 6,419,931 340 HPV16 E7 GTLGIVCPI U.S. 6,419,931 341HPV16 E7 MLDLQPETT U.S. 6,419,931 342 HPV16 E6 TIHDIILECV U.S. 6,419,931343 HIV VLAEAMSQV U.S. 6,419,931 344 HIV LLWKGEGAVV U.S. 6,419,931 345HIV LLWKGEGAV U.S. 6,419,931 346 HIV ILKEPVHGV U.S. 6,419,931 347 HIVIVGAETFYV U.S. 6,419,931 348 HIV IIGAETFYV U.S. 6,419,931 349 HIVLWVTVYYGV U.S. 6,419,931 350 HIV LMVTVYYGV U.S. 6,419,931 351 HBc 11-27ATVELLSFLPSDFFPSV U.S. 6,419,931 352 HBc 91-110Thr-Asn-Met-Gly-Leu-Lys-Phe-Arg-Gln- U.S. 6,322,789*Leu-Leu-Trp-Phe-His-Ile-Ser-Cys-Leu- Thr-Phe 353 HBenv 329-348Ala-Ser-Ala-Arg-Phe-Ser-Trp-Leu-Ser- U.S. 6,322,789Leu-Leu-Val-Pro-Phe-Val-Gln-Trp-Phe- Val-Gly 354 HBenv 349-368Leu-Ser-Pro-Thr-Val-Trp-Leu-Ser-Val- U.S. 6,322,789Ile-Trp-Met-Met-Trp-Tyr-Trp-Gly-Pro- Ser-Leu 355 HBenv 309-328Asn-Cys-Thr-Cys-Ile-Pro-Ile-Pro-Ser- U.S. 6,322,789Ser-Trp-Ala-Phe-Gly-Lys-Phe-Leu-Trp- Glu-Trp 356 HBenv 329-358Ala-Ser-Ala-Arg-Phe-Ser-Trp-Leu-Ser- U.S. 6,322,789Leu-Leu-Val-Pro-Phe-Val-Gln-Trp-Phe- Val-Gly 357 HBc 91-102Thr-Asn-Met-Gly-Leu-Lys-Phe-Arg-Gln- U.S. 6,322,789Leu-Leu-Trp-Leu-Ser-Pro-Thr-Val-Trp- Leu-Ser-Val-Ile- 358 HBc 128-140TPPAYRPPNAPIL U.S. 6,419,931 359 HBenv 360-368 WMMWYWGPSL U.S. 6,322,789360 Myobacterium LEDPYEKIGAELVKEV leprae 361 MyobacteriumEQIAATAAISAGDQS U.S. Ser. No. 11/041,893* leprae 362 MyobacteriumAGDQSIGDLIAEAMD U.S. Ser. No. 11/041,893 leprae 363 MyobacteriumVEGAGDTDAIAGRVA U.S. Ser. No. 11/041,893 leprae 364 MyobacteriumAGGVAVIKAGAATEV U.S. Ser. No. 11/041,893 leprae 365 MyobacteriumGDEATGANIVKVALE U.S. Ser. No. 11/041,893 leprae 366 MyobacteriumLQNAASIAGLFLTTE U.S. Ser. No. 11/041,893 leprae 367 MyobacteriumAGGGVTLLQAAPALD U.S. Ser. No. 11/041,893 leprae 368 MyobacteriumRVAQIRTEIENSD U.S. Ser. No. 11/041,893 leprae 369 MyobacteriumLLQAAPALDKLKL U.S. Ser. No. 11/041,893 leprae 370 MyobacteriumPEKTAAPASDPTG U.S. Ser. No. 11/041,893 leprae 371 MyobacteriumLEDPYEKIGAELVKEV U.S. Ser. No. 11/041,893 tuberculosis 372 MyobacteriumEQIAATAAISAGDQS U.S. Ser. No. 11/041,893 tuberculosis 373 MyobacteriumAGDQSIGDLIAEAMD U.S. Ser. No. 11/041,893 tuberculosis 374 MyobacteriumVEGAGDTDAIAGRVA U.S. Ser. No. 11/041,893 tuberculosis 375 MyobacteriumAGGVAVIKAGAATEV U.S. Ser. No. 11/041,893 tuberculosis 376 MyobacteriumGDEATGANTVKVALE U.S. Ser. No. 11/041,893 tuberculosis 377 MyobacteriumLQNAASIAGLFLTTE U.S. Ser. No. 11/041,893 tuberculosis 378 MyobacteriumAGGGVTLLQAAPALD U.S. Ser. No. 11/041,893 tuberculosis 379 MyobacteriumRVQAQIRTEIENSD U.S. Ser. No. 11/041,893 tuberculosis 380 MyobacteriumLLQAAPALDKLKL U.S. Ser. No. 11/041,893 tuberculosis 381 MyobacteriumLPAKFLEGF U.S. Ser. No. 11/041,893 tuberculosis 382 MyobacteriumYLQVPSPSMGRDIKVQFQ U.S. Ser. No. 11/041,893 tuberculosis 383Myobacterium GRDIKVQFQSGGNNSPAV U.S. Ser. No. 11/041,893 tuberculosis384 Myobacterium GCQTYKEWTLLTSELPQW U.S. Ser. No. 11/041,893tuberculosis 385 Myobacterium IPAEFLENF U.S. Ser. No. 11/041,893tuberculosis 386 Myobacterium WPTLIGLAM U.S. Ser. No. 11/041,893tuberculosis 387 Myobacterium IPAKFLEGL U.S. Ser. No. 11/041,893tuberculosis 388 Myobacterium MPVGGQSSF U.S. Ser. No. 11/041,893tuberculosis 389 Myobacterium MPVGGQSSFY U.S. Ser. No. 11/041,893tuberculosis 390 Myobacterium MSQIMYNYPAMMAHAGDMU.S. Ser. No. 11/041,893 tuberculosis 391 Myobacterium ITYQGWQTQWNQALEDU.S. Ser. No. 11/041,893 tuberculosis 392 Myobacterium ATFAAPVALAAU.S. Ser. No. 11/041,893 tuberculosis 393 Myobacterium SGATIPQGEQSU.S. Ser. No. 11/041,893 tuberculosis 394 MyobacteriumAVAASNNPELTTLTAALSGQLNPQV U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 395 Myobacterium ALSGQLNPQVNLVDTLNSGQYU.S. Ser. No. 11/041,893 tuberculosis/ Mycobacterium bovis 396Myobacterium FSKLPASTIDELKTNSSLLTSILTYH U.S. Ser. No. 11/041,893tuberculosis/ Mycobacterium bovis 397 MyobacteriumGNADVVCGGVSTANATVYMIDSVL U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 398 Myobacterium AVAASNNPELTTLTAALSGQLNPQVU.S. Ser. No. 11/041,893 tuberculosis/ Mycobacterium bovis 399Myobacterium ALSGQLNPQVNLVDTLNSGQY U.S. Ser. No. 11/041,893tuberculosis/ Mycobacterium bovis 400 MyobacteriumFSKLPASTIDELKTNSSLLTSILTYH U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 401 Myobacterium GNADVVCGGVSTANATVYMIDSVLU.S. Ser. No. 11/041,893 tuberculosis/ Mycobacterium bovis 402Myobacterium ATTVYMIDSVLMPPA U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 403 Myobacterium MTEQQWNFAGIEAAASAIQGU.S. Ser. No. 11/041,893 tuberculosis/ Mycobacterium bovis 404Myobacterium EQQWNFAGIEAAA U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 405 Myobacterium WNFAGIEAA U.S. Ser. No. 11/041,893tuberculosis/ Mycobacterium bovis 406 Myobacterium VQGVQQKWDATATELNNALQU.S. Ser. No. 11/041,893 tuberculosis/ Mycobacterium bovis 407Myobacterium AWGGSGSEAUQGVQQKWDATATEL U.S. Ser. No. 11/041,893tuberculosis/ Mycobacterium bovis 408 MyobacteriumQGVQQKWDATATELNNALQNLART U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 409 Myobacterium LARTISEAGQAMASTEGNVTGMFAU.S. Ser. No. 11/041,893 tuberculosis/ Mycobacterium bovis 410Myobacterium EQQWNFAGIEAAA U.S. Ser. No. 11/041,893 tuberculosis/Mycobacterium bovis 411 Streptococcus NNNDVNIDRTLVAKQSVVKFU.S. Ser. No. 11/041,893 mutans 412 Streptococcus QLKTADLPAGRDETTSFVLVU.S. Ser. No. 11/041,893 mutans 413 Streptococcus LATFNADLTKSVATIYPTVVU.S. Ser. No. 11/041,893 mutans 414 Chlamydia GDYVFDRIU.S. Ser. No. 11/041,893 pneumoniae 415 Chlamydia SLLGNATALU.S. Ser. No. 11/041,893 pneumoniae 416 Chlamydia QAVANGGAIU.S. Ser. No. 11/041,893 pneumoniae 417 Chlamydia RGAFCDKEFU.S. Ser. No. 11/041,893 pneumoniae 418 Chlamydia CYGRLYSVKVU.S. Ser. No. 11/041,893 pneumoniae 419 Chlamydia KYNEEARKKIU.S. Ser. No. 11/041,893 pneumoniae 420 Chlamydia GPKGRHVVIU.S. Ser. No. 11/041,893 pneumoniae 421 Escherichia coli TPHPARIGLU.S. Ser. No. 11/041,893 422 Salmonella LIQCMLKKTMLSINQU.S. Ser. No. 11/041,893 typhimurium 423 Listeria GYKDGNEYIU.S. Ser. No. 11/041,893 monocytogenes 424 Borrelia VVKEGTVTLSKNISKSGEVSU.S. Ser. No. 11/041,893 burgdorferi 425 Lymphocytic FQPQNGQFIU.S. Ser. No. 11/041,893 choriomeningitis virus 426 LymphocyticRPQASGVYM U.S. Ser. No. 11/041,893 choriomeningitis virus 427Lymphocytic PYIACRTSI U.S. Ser. No. 11/041,893 choriomeningitis virus428 Lymphocytic MYPIACRTSI U.S. Ser. No. 11/041,893 choriomeningitisvirus 429 Lymphocytic WPYIACRTSI U.S. Ser. No. 11/041,893choriomeningitis virus 430 Lassa Fever virus FGTMPSLTLACLTU.S. Ser. No. 11/041,893 431 Lassa Fever virus FGMPSLTIACMCU.S. Ser. No. 11/041,893 432 Lassa Fever virus QGQVDLNDAVQALU.S. Ser. No. 11/041,893 433 Lassa Fever virus QGQADLNDVIQSLU.S. Ser. No. 11/041,893 434 Lassa Fever virus ALGMFISDTPGERU.S. Ser. No. 11/041,893 435 Lassa Fever virus SLGMFVSDTPGERU.S. Ser. No. 11/041,893 436 Lassa Fever virus QLDPNAKTWMDIEU.S. Ser. No. 11/041,893 437 Lassa Fever virus NLIPNAKTWMDIEU.S. Ser. No. 11/041,893 438 Lassa Fever virus VWDQFKDLCHMHTU.S. Ser. No. 11/041,893 439 Lassa Fever virus VWDQFKDLCHMHTU.S. Ser. No. 11/041,893 440 Lassa Fever virus IWDEYKHLCRMHTU.S. Ser. No. 11/041,893 441 HIV-1 FPVTPQVP U.S. Ser. No. 11/041,893 442HIV-1 FPVTPRVPL U.S. Ser. No. 11/041,893 443 HIV-1 TPQVPLRPMU.S. Ser. No. 11/041,893 444 HIV-1 YPLTFGWCY U.S. Ser. No. 11/041,893445 HIV-1 PLTFGWCYK U.S. Ser. No. 11/041,893 446 HIV-1 LTFGWCYKLU.S. Ser. No. 11/041,893 447 HIV-1 EIYKRWIIL U.S. Ser. No. 11/041,893448 HIV-1 ILGLNKIV U.S. Ser. No. 11/041,893 449 HIV-1 ILGLNKIVRMYU.S. Ser. No. 11/041,893 450 HBV sAg QAGFFLLTRILTIPQSLDU.S. Ser. No. 11/041,893 451 HBV sAg SCCCTKPTDGNCTCIPIPSSU.S. Ser. No. 11/041,893 452 HBV sAg WEWASVRFSWLSU.S. Ser. No. 11/041,893 453 HBV sAg LPLLPIFFCLWVYIU.S. Ser. No. 11/041,893 454 HPV RAHYNIVTF U.S. Ser. No. 11/041,893 455HPV GQAEPDRAHYNIVTFCCKCDSTLRLC U.S. Ser. No. 11/041,893 VQSTHVDIR 456EBV RRIYDLIEL U.S. Ser. No. 11/041,893 457 EBV RKIYDLIELU.S. Ser. No. 11/041,893 458 EBV FRKAQIQGL U.S. Ser. No. 11/041,893 459EBV HRCQAIRK U.S. Ser. No. 11/041,893 460 EBV RRARSLSAERYU.S. Ser. No. 11/041,893 461 EBV DWTGGALLVLYSFALMLU.S. Ser. No. 11/041,893 462 EBV ALLVLYSFAL U.S. Ser. No. 11/041,893 463EBV LLVLYSFAL U.S. Ser. No. 11/041,893 464 EBV VLYSFALMLU.S. Ser. No. 11/041,893 465 EBV LVLGIWIYLLEMLWRRLGU.S. Ser. No. 11/041,893 466 EBV LIIALYLQQNWWTLLVDU.S. Ser. No. 11/041,893 467 EBV IALYLQQNW U.S. Ser. No. 11/041,893 468EBV ALYLQQNWW U.S. Ser. No. 11/041,893 469 EBV QNWWTLLVDU.S. Ser. No. 11/041,893 470 EBV LYLQQNWWT U.S. Ser. No. 11/041,893 471EBV LIWMYYHGQRHSDEHHH U.S. Ser. No. 11/041,893 472 EBV QRHSDEHHHU.S. Ser. No. 11/041,893 473 EBV GQRHSDEHH U.S. Ser. No. 11/041,893 474EBV YYHGQRHSD U.S. Ser. No. 11/041,893 475 EBV WMYYHGQRHU.S. Ser. No. 11/041,893 476 EBV TDDSGHESDSNSNEGRHU.S. Ser. No. 11/041,893 477 EBV ESDSNSNEG U.S. Ser. No. 11/041,893 478EBV DSNSNEGRH U.S. Ser. No. 11/041,893 479 EBV PHSPSDSAGNDGGPPQLU.S. Ser. No. 11/041,893 480 EBV AGNDGGPPQ U.S. Ser. No. 11/041,893 481EBV PSDSAGNDG U.S. Ser. No. 11/041,893 482 EBV RHSDEHHHDDSLPHPQQU.S. Ser. No. 11/041,893 483 EBV EENLLDVFRM U.S. Ser. No. 11/041,893 484EBV LVSDYCNVLNKEFTA U.S. Ser. No. 11/041,893 485 EBV FFIQQAPSNRVMIPATU.S. Ser. No. 11/041,893 486 EBV RVMIPATIGTAMYKLU.S. Ser. No. 11/041,893 487 EBV KHSRVRAYTYSKVLGU.S. Ser. No. 11/041,893 488 EBV RALIKTLPRASYSSHU.S. Ser. No. 11/041,893 489 EBV ERPIFPHPSKPTFLPU.S. Ser. No. 11/041,893 490 EBV EVCQPRKIRPFHPPGU.S. Ser. No. 11/041,893 491 EBV QKEEAAICGQMDDLSHU.S. Ser. No. 11/041,893 492 EBV DYCNVLNKEF U.S. Ser. No. 11/041,893 493EBV ATIGTAMYK U.S. Ser. No. 11/041,893 494 EBV FLRGRAYGLU.S. Ser. No. 11/041,893 495 EBV AVFDRKSDAK U.S. Ser. No. 11/041,893 496EBV RRIYLDLIEL U.S. Ser. No. 11/041,893 497 EBV LLWTLVVLLU.S. Ser. No. 11/041,893 498 EBV CLGGLLTMV U.S. Ser. No. 11/041,893 499EBV IEDPPFNSL U.S. Ser. No. 11/041,893 500 EBV SSCSSCPLSKIU.S. Ser. No. 11/041,893 501 EBV TYGPVFMCL U.S. Ser. No. 11/041,893 502EBV APENAYQAY U.S. Ser. No. 11/041,893 503 EBV RAKFKQLLU.S. Ser. No. 11/041,893 504 EBV GLCTLVAML U.S. Ser. No. 11/041,893 505EBV TLDYKPLSV U.S. Ser. No. 11/041,893 506 EBV QNGALAINTEU.S. Ser. No. 11/041,893 507 EBV EENLLDFVRF U.S. Ser. No. 11/041,893 508EBV HPLTNNLPL U.S. Ser. No. 11/041,893 509 HCV GYKVLVLNPSVAATU.S. Ser. No. 11/041,893 510 Hantaan virus NAHEGQLVIU.S. Ser. No. 11/041,893 511 Hantaan virus ISNQEPLKLU.S. Ser. No. 11/041,893 512 Dengue virus LIGFRKEIGRMLNILU.S. Ser. No. 11/041,893 513 Dengue virus KGPLRMVLAFITFLRU.S. Ser. No. 11/041,893 514 Rotavirus RNFDTIRLSFQLVERU.S. Ser. No. 11/041,893 515 Rotavirus RLSFQLVRPPNMTPU.S. Ser. No. 11/041,893 516 Rotavirus VRPPNMTPAVANLFU.S. Ser. No. 11/041,893 517 Measles virus LSEIKGVIVHRLEAVU.S. Ser. No. 11/041,893 518 Trypanosoma IYNVGQVSIU.S. Ser. No. 11/041,893 cruzi 519 Trypanosoma SHNFTLVASVIIEEAU.S. Ser. No. 11/041,893 cruzi 520 Trypanosoma LVASVIIEEAPSGNTU.S. Ser. No. 11/041,893 cruzi 521 Toxoplasma TDPGDVVIEELFNRIPETSVU.S. Ser. No. 11/041,893 gondii 522 Toxoplasma LQLIRLAASLQHYGLVHAU.S. Ser. No. 11/041,893 gondii 523 Toxoplasma IEWIYRRCKNIPQPVRALLEGFLRU.S. Ser. No. 11/041,893 gondii 524 Babesia bovis EYLVNKVLYMATMNYKTU.S. Ser. No. 11/041,893 525 Babesia bovis EAPWYKRWIKKFRU.S. Ser. No. 11/041,893 526 Babesia bovis FREAPQATKHFLU.S. Ser. No. 11/041,893 527 Babesia bovis FREAPQATKHFLDENU.S. Ser. No. 11/041,893 528 Babesia bovis FREAPQATKHFLGENU.S. Ser. No. 11/041,893 529 Babesia bovis FVVSLLKKNVVRDPESNDVENFASQYU.S. Ser. No. 11/041,893 FYM 530 Babesia bovis VNSEKVDADDAGNAETQQLPDDAENU.S. Ser. No. 11/041,893 EVRADD 531 Plasmodium NFVGKFLELQIPGHTDLLHLU.S. Ser. No. 11/041,893 vivax 532 Plasmodium FNQLMHVINFHYDLLRANVHU.S. Ser. No. 11/041,893 vivax 533 Plasmodium LDMLKKVVLGLWKPLDNIKDU.S. Ser. No. 11/041,893 vivax 534 Plasmodium LEYYLREKAKMAGTLIPESU.S. Ser. No. 11/041,893 vivax 535 Plasmodium KKIKAFLETSNNKAAAPAQSU.S. Ser. No. 11/041,893 vivax 536 Plasmodium SKDQIKKLTSLKNKLERRQNU.S. Ser. No. 11/041,893 vivax 537 Plasmodium DPNANPNVDPNANPNVU.S. Ser. No. 11/041,893 falciparum 538 PlasmodiumFGYRKPLDNIKDNVGKMEDYIKK U.S. Ser. No. 11/041,893 falciparum 539Plasmodium SKLNSLNNPHNVLQNFSVFFNKK U.S. Ser. No. 11/041,893 falciparum540 Plasmodium GYRKPLDNIKDNVGKMEDYIKK U.S. Ser. No. 11/041,893falciparum 541 Plasmodium KLNSLNNPHNVLQNFSVFFNK U.S. Ser. No. 11/041,893falciparum 542 Plasmodium TKILLKHYKGLVKYYNGESSP U.S. Ser. No. 11/041,893falciparum 543 Plasmodium HGTKYLIDGYEEINELLYKLN U.S. Ser. No. 11/041,893falciparum 544 Plasmodium VTHESYQELVKKLEALEDAV U.S. Ser. No. 11/041,893falciparum 545 Plasmodium GLFHKEKMILNEEEITTKGA U.S. Ser. No. 11/041,893falciparum 546 Plasmodium DSNIMNSINNVMDEIDFFEK U.S. Ser. No. 11/041,893falciparum 547 Plasmodium DDYTEYDLTEIDNILVKMFKTNU.S. Ser. No. 11/041,893 falciparum 548 Plasmodium LTMSNVKNVSQTNFKSLLRNLU.S. Ser. No. 11/041,893 falciparum 549 Plasmodium HTLETVNISDVNDFQISKYU.S. Ser. No. 11/041,893 falciparum 550 Plasmodium DDEEDLDEFKPIVQYDNFQDU.S. Ser. No. 11/041,893 falciparum 551 Plasmodium EENIGIKELEDLIEKNENLU.S. Ser. No. 11/041,893 falciparum 552 Plasmodium DDLDEGIEKSSEELSEEKU.S. Ser. No. 11/041,893 falciparum 553 Plasmodium IKKGKKYEKTKDNNFU.S. Ser. No. 11/041,893 falciparum 554 PlasmodiumDNEILQIVDELSEDITKYFMKL U.S. Ser. No. 11/041,893 falciparum 555Plasmodium EQQQSDLEQERLAKEKLQEQQSDLEQ U.S. Ser. No. 11/041,893falciparum ERRAKEKLQ *The listed patents and patent applications arehereby expressly incorporated by reference in their entirety.

Yet other exemplary TCEs are listed in TABLES 4 as well as describedherein (e.g., SEQ ID NOs: 809-1011 and SEQ ID NO:1014).

TABLE 4 HCV T-CELL EPITOPES SEQ HLA ID Protein Restriction Sequence NO:Core A2 FLPSDFFPSV 809 Core A2 CLTFGRETV 810 Core A2 VLEYLVSFGV 811 CoreA2/A24 EYLVSFGVW 812 Core A2 ILSTLPETTV 813 Core A33/A68 STLPETTVVRR 814Core A2 AILSKTGDPV 815 Env A2 LLDPRVRGL 816 Env A2 VLQAGFFLL 817 Env A2FLLTRILTI 818 Env A2 SLNFLGGTTV 819 Env A2 FLGGTPVCL 820 Env A2LLLCLIFLL 821 Env A2 LLCLIFLLV 822 Env A2 LLDYQGMLPV 823 Env A2LVLLDYQGML 824 Env A2 VLLDYQGML 825 Env A2 LLDYQGMLPV 826 Env A2WLSLLVPFV 827 Env A2 LLVPFVQWFV 828 Env A2 GLSPTVWLSV 829 Env A2SIVSPFIPLL 830 Env A2 LLPIFFCLWV 831 Env A2 ILSPFFFLPLL 832 x-Protein A2VLCLRPVGA 833 x-Protein A2 TLPSPSSSA 834 x-Protein A2 HLSLRGLFV 835x-Protein A2 VLHKRTLGL 836 x-Protein A2 AMSTTDLEA 837 x-Protein A2CLFKDWEEL 838 Pol A24 LYSSTVPVF 839 Pol A2 GLSRYVARL 840 Pol A2YMDDVVLGA 841 Pol A2 FLLSLGIHL 842 Pol A24 KYTSFPWLL 843 Pol A2ILRGTSFVYV 844 Pol A2 SLYADSPSV 845

Other exemplary sequences that can be used in part or in whole asepitopes in the embodiments are also described herein, e.g., TCE's andBCE's.

Other exemplary HTL epitopes within a HTL peptide from tetanus toxoid830-843 having the sequence:Gln-Tyr-Ile-Lys-Ala-Asn-Ser-Lys-Phe-Ile-Gly-Ile-Thr-Glu (QYIKANSKFIGITE)[SEQ ID NO: 556], malaria circumsporozoite 382-398 (KIAKMEKASSVFNVVNS)[SEQ ID NO: 557]; malaria circumsporozoite 378-398(DIEKKIAKMEKASSVFNVVNS) [SEQ ID NO: 558], malaria circumsporozoite326-345 (EYLNKIQNSLSTEWSPCSVT) and ovalbumin 323-336Ile-Ser-Gln-Ala-Val-His-Ala-Ala-His-Ala-Glu-Ile-Asn-Glu [SEQ ID NO:559]and the influenza epitope 307-319Pro-Lys-Tyr-Val-Lys-Gln-Asn-Thr-Leu-Lys-Leu-Ala-Thr [SEQ ID NO: 560];Corneybacterium diptheriae diphtheria toxin NLFQVVHWSYNRPAYSPGYV [SEQ IDNO: 561]; Escherichia coli OmpF FDFGLRPSTAYTKSKAKDVVE [SEQ ID NO: 567];Escherichia coli OmpF DEVFATYYFNKNMSTYVDYII [SEQ ID NO: 1379];Escherichia coli OmpF NKNMSTYVDYIINQIDSKNK [SEQ ID NO: 568]. Inaddition, suitable T helper peptides have been identified as describedin pending U.S. patent application Ser. No. 08/121,101, hereby expresslyincorporated by reference in its entirety.

Other examples of HTL-inducing peptides are those which are specific forthe antigen (virus or other organism, tumor, etc.) being targeted by theCTL. For example, several HTL-inducing peptides specific for HBV havebeen described, such as HBc₁₋₂₀, having the sequence:Met-Asp-Ile-Asp-Pro-Tyr-Lys-Glu-Phe-Gly-Ala-Thr-Val-Glu-Leu-Leu-Ser-Phe-Leu-Pro[SEQ ID NO: 562]; peptides from the region HBc₅₀₋₆₉, which has thesequencePro-His-His-Tyr-Ala-Leu-Arg-Gln-Ala-Ile-Leu-Cys-Trp-Gly-Glu-Leu-Met-Tyr-Leu-Ala[SEQ ID NO: 563], and from the region of HBc₁₀₀₋₁₃₉, includingHBc₁₀₀₋₁₁₉ having the sequenceLeu-Leu-Trp-Phe-His-Ile-Ser-Cys-Leu-Thr-Phe-Gly-Arg-Glu-Thr-Val-Ile-Glu-Tyr-Leu[SEQ ID NO: 564] (where Ile₁₁₆ is Leu in the HBV adw subtype),HBc₁₁₇₋₁₃₁ having the sequenceGlu-Tyr-Leu-Val-Ser-Phe-Gly-Val-Trp-Ile-Arg-Thr-Pro-Pro-Ala [SEQ ID NO:565], and peptide HBc₁₂₀₋₁₃₉ having the sequenceVal-Ser-Phe-Gly-Val-Trp-Ile-Arg-Thr-Pro-Pro-Ala-Tyr-Arg-Pro-Pro-Asn-Ala-Pro-Ile[SEQ ID NO: 566]. See, Ferrari et al., J. Clin. Invest. 88:214-222(1991), and U.S. Pat. No. 4,882,145, and U.S. Pat. No. 5,143,726, herebyexpressly incorporated by reference in their entireties.

The skilled artisan will also appreciate that proteins containing atleast one epitope, such as a TCE, useful in the embodiments discloseherein can be identified using a variety of techniques known in the art.Illustrative methods are described in, for example, Current Protocols inImmunology, Edited by: John E. Coligan, Ada M. Kruisbeek, David H.Margulies, Ethan M. Shevach, Warren Strober (2001 John Wiley & Sons, NY,N.Y.) Ausubel et al. (2001 Current Protocols in Molecular Biology,Greene Publ. Assoc. Inc. & John Wiley & Sons, Inc., NY, N.Y.); Sambrooket al. (1989 Molecular Cloning, Second Ed., Cold Spring HarborLaboratory, Plainview, N.Y.); Maniatis et al. (1982 Molecular Cloning,Cold Spring Harbor Laboratory, Plainview, N.Y.). Illustrative methodsuseful in this context include intracellular cytokine staining (ICS),ELISPOT, proliferation assays, cytotoxic T cell assays includingchromium release or equivalent assays, and gene expression analysisusing any number of polymerase chain reaction (PCR) or RT-PCR basedassays.

Epitopes of the embodiments disclosed herein may be identified using anynumber of techniques known in the art, such as those described by: LambJ R, et al., (1989) Rev. Infect. Dis. March-April: Suppl 2:s443-447;Lamb J R, et al. (1987) EMBO J. 6(5):1245-1249; Lamb J R, et al., (1986)Lepr. Rev. Dec.; Suppl 2:131-137; Mehra V, et al., (1986) Proc. Natl.Acad. Sci. USA 83(18): 7013-7; Horsfall A C, et al., (1991) Immunol.Today 12(7):211-3; Rothbard J B et al., (1990) Curr Top MicrobiolImmunol 155:143-52; Singh H et al., (2001) Bioinformatics 17:1236-1237;DeGroot A S, et al. Vaccine 19:4385-4395; DeLalla C, et al., (1999) J.Immunol. 163:1725-1729; Cochlovius B, et al., (2000) J. Immunol.165:4731-4741; Consogno G, et al. (2003) Blood 101:1039-1044; Roberts CG, et al. (1996) AIDS Res. Hum. Retrovir. 12:593-610; Kwok W, et al.(2001) Trends Immunol. 22:583-588; Novak E J, et al., (2001) J. Immunol.166:6665-6670.

An epitope that is used in some embodiments described herein maycomprise a naturally occurring or naturally processed epitope as definedusing any number of assays known to the skilled artisan and as describedherein. Assays for identifying epitopes are known to the skilled artisanand are described, for example, in Current Protocols in Immunology, JohnE. Coligan, Ada M. Kruisbeek, David H. Margulies, Ethan M. Shevach, andWarren Strober (Eds), John Wiley & Sons, New York. N.Y. Epitopes may beidentified using intracellular cytokine staining and flow cytometricanalysis such as described in Hoffmeister B., et al., (2003) Methods.;29(3):270-281; Maecker H T, et al., (2001) J Immunol Methods255(1-2):27-40. Similarly, proteins, peptides, overlapping peptides, orpools of peptides can be used in standard chromium release and/orproliferation assays to identify epitopes.

In those cases where antigen-specific T cell lines or clones areavailable, for example tumor-infiltrating lymphocytes (TIL) orvirus-specific CTL, these cells can be used to screen for the presenceof the relevant epitopes using target cells prepared with specificantigens. Such targets can be prepared using random, or selectedsynthetic peptide libraries, which would be utilized to sensitize thetarget cells for lysis by the CTL. Another approach to identify therelevant epitope when T cell lines or clones are available is to userecombinant DNA methodologies. Gene, or preferably cDNA, libraries fromCTL-susceptible targets are first prepared and transfected intonon-susceptible target cells. This allows the identification and cloningof the gene coding the protein precursor to the peptide containing theCTL epitope. The second step in this process is to prepare truncatedgenes from the relevant cloned gene, in order to narrow down the regionthat encodes for the CTL epitope. This step is optional if the gene isnot too large. The third step is to prepare synthetic peptides ofapproximately 10-20 amino acids of length, overlapping by 5-10 residues,which are used to sensitize targets for the CTL. When a peptide, orpeptides, is shown to contain the relevant epitope, smaller peptides canbe prepared to establish the peptide of minimal size that contains theepitope.

Alternatively, epitopes may be defined by direct elution of peptidesbound by particular MHC molecule and direct sequencing of the peptides(see, for example, Engelhard V H, et al., Cancer J. 2000 May; 6 Suppl.3:S272-80). Briefly, the eluted peptides are separated using apurification method such as HPLC, and individual fractions are testedfor their capacity to sensitize targets for CTL lysis or to induceproliferation of cytokine secretion in HTL. When a fraction has beenidentified as containing the peptide, it is further purified andsubmitted to sequence analysis. The peptide sequence can also bedetermined using tandem mass spectrometry. A synthetic peptide is thenprepared and tested with the CTL or HTL to corroborate that the correctsequence and peptide have been identified

Epitopes may also be identified using computer analysis, such as theTsites program, which searches for peptide motifs that have thepotential to elicit Th responses. (See, e.g., Rothbard and Taylor,(1988) EMBO J. 7:93-100; Deavin et al., (1996) Mol. Immunol. 33:145-155,1996). CTL peptides with motifs appropriate for binding to murine andhuman class I or class II MHC may be identified according to BIMAS(Parker et al., (19944) J. Immunol. 152:163) and other HLA peptidebinding prediction analyses. Briefly, the protein sequences for examplefrom viral or tumor cell components are examined for the presence ofMHC-binding motifs. These binding motifs which exist for each MHC alleleare conserved amino acid residues, usually at positions 2 (or 3) and 9(or 10) for MHC class I binding peptides of 9-10 residues long.Synthetic peptides are then prepared of those sequences bearing the MHCbinding motifs, and subsequently are tested for their ability to bind toMHC molecules. The MHC binding assay can be carried out either usingcells which express high number of empty MHC molecules (cellular bindingassay), or using purified MHC molecules. Lastly, the MHC bindingpeptides are then tested for their capacity to induce a CTL response innaive individuals, either in vitro using human lymphocytes, or in vivousing HLA-transgenic animals. These CTL are tested usingpeptide-sensitized target cells, and targets that naturally process theantigen, such as viral infected cells or tumor cells. To further confirmimmunogenicity, a peptide may be tested using an HLA A2 transgenic mousemodel and/or any of a variety of in vitro stimulation assays.

Epitopes that are used with embodiments described herein may also beidentified using a peptide motif searching program based on algorithmsdeveloped by Rammensee, et al. (Hans-Georg Rammensee, Jutta Bachmann,Niels Nikolaus Emmerich, Oskar Alexander Bachor, Stefan Stevanovic:SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics(1999) 50: 213-219); by Parker, et. al. (supra), or using methods suchas those described by Doytchinova and Flower (2002) Immunol Cell Biol.80(3):270-9 and Blythe M J, Doytchinova I A, Flower D R. (2002),Bioinformatics 18, 434-439.

In certain embodiments, an epitope may comprise a variant of a nativeepitope. A “variant,” as used herein, is a polypeptide (or a nucleicacid encoding such a polypeptide) that differs from a native polypeptidein one or more substitutions, deletions, additions and/or insertions,such that the immunogenicity of the polypeptide is retained (i.e., theability of the variant to react with antigen-specific antisera and/orT-cell lines or clones is not substantially diminished relative to thenative polypeptide). In other words, the ability of a variant to reactwith antigen-specific antisera and/or T-cell lines or clones may beenhanced or unchanged, relative to the native polypeptide, or may bediminished by less than 50%, and preferably less than 20% relative tothe native polypeptide. In some embodiments, the ability of a variant toreact with antigen-specific antisera and/or T-cell lines or clones maybe diminished by less than 30%, 25%, 20%, 19%, 18%, 17%, 16%, 15%, 10%,9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, or 0.5%, relative to the nativepolypeptide. In one embodiment the ability of a variant to react withantigen-specific antisera and/or T-cell lines or clones may be enhancedby at least 30%, 25%, 20%, 19%, 18%, 17%, 16%, 15%, 10%, 9%, 8%, 7%, 6%,5%, 4%, 3%, 2%, 1%, or 0.5%, relative to the native polypeptide. Suchvariants may generally be identified by modifying one of the abovepolypeptide sequences and evaluating the reactivity of the modifiedpolypeptide with antisera and/or T-cells as described herein. In someembodiments, a variant may be identified by evaluating its ability tobind to a human, murine, or nonhuman primate MHC molecule. In preferredembodiments, a variant polypeptide has a modification such that theability of the variant polypeptide to bind to a class I or class II MHCmolecule is increased relative to that of a wild type (unmodified)polypeptide. The skilled artisan recognizes that any number of class Ior class II MHC molecules can be used in the context of the embodimentsdescribed herein, for example any HLA molecule as identified andavailable from the IMGT/HLA database.

In more embodiments, the ability of the variant TCE to bind to an HLAmolecule is increased by at least 2 fold, preferably at least 3 fold, 4fold, or 5 fold relative to that of a native polypeptide. It has beenfound in some embodiments that a relatively small number ofsubstitutions (e.g., 1 to 3) within an epitope can enhance the abilityof the epitope to elicit an immune response. Suitable substitutions maygenerally be identified by using computer programs, as described above,and the effect can be confirmed based on the reactivity of the modifiedpolypeptide with antisera and/or T-cells as described herein.Accordingly, within certain preferred embodiments, a variant in which 1to 3 amino acid resides within an epitope are substituted such that theability to react with antigen-specific antisera and/or T-cell lines orclones is statistically greater than that for the unmodifiedpolypeptide. Such substitutions are preferably located within an MHCbinding site of the polypeptide, which may be identified as describedabove. Preferred substitutions allow increased binding to MHC class I orclass II molecules.

The CTL or HTL sequences employed in the compositions and methodsdescribed herein need not be identical to specific amino acids disclosedin aforementioned disclosures, and can be selected by a variety oftechniques, for example, according to certain motifs as described above.Therefore, the epitopes may be subject to various changes, such asinsertions, deletions, and substitutions, either conservative ornon-conservative, where such changes might provide for certainadvantages in their use. Conservative substitutions are discussed abovein reference to TABLE 1. Usually, the portion of the sequence which isintended to substantially mimic a CTL or HTL stimulating epitope willnot differ by more than about 20% from the corresponding sequence of anative, or naturally occurring antigen, when known, except whereadditional amino acids may be added at either terminus for the purposeof modifying the physical or chemical properties of the peptide for,e.g., ease of linking or coupling, and the like. In those situationswhere regions of the peptide sequences are found to be polymorphic amongantigen subtypes, it may be desirable to vary one or more particularamino acids to more effectively mimic differing CTL or HTL epitopes ofdifferent antigen strains.

In some instances, it may be desirable to combine two or more epitopesthat contribute to stimulating specific CTL or HTL responses in one ormore patients or histocompatibility types. The epitopes in thecomposition can be identical or different, and together they can provideequivalent or greater biological activity than the parent peptide(s).For example, using the methods described herein, two or more peptidesmay define different or overlapping CTL epitopes from a particularregion, e.g., the peptide region, e.g., HBenv₃₀₉₋₃₂₈; peptide regionHBenv₃₂₉₋₃₄₉, HBenv₃₄₉₋₃₆₈, or peptide region HBc₉₁₋₁₁₀, which peptidescan be combined in a “cocktail” to provide enhanced immunogenicity ofCTL responses, and peptides can be combined with peptides havingdifferent MHC restriction elements.

Compositions

As will be understood by those skilled in the art, the nucleic acids ofthe embodiments disclosed herein can be single-stranded (coding orantisense), or double-stranded, and may be a DNA (genomic, cDNA, orsynthetic) or RNA molecule. Additional coding or non-coding sequencesmay, but need not, be present within a nucleic acid of the embodimentsdisclosed herein, and a nucleic acid may, but need not, be linked toother molecules and/or support materials.

Embodiments of the invention also include (a) DNA vectors that containany of the foregoing nucleic acid sequence and/or their complements(i.e., antisense); (b) DNA expression vectors that contain any of theforegoing nucleic acid sequences operatively associated with aregulatory element that directs the expression of the nucleic acid; and(c) genetically engineered host cells that contain any of the foregoingnucleic acid sequences operatively associated with a regulatory elementthat directs the expression of the coding sequences in the host cell.These recombinant constructs are capable of replicating autonomously ina host cell. Alternatively, the recombinant constructs can becomeintegrated into the chromosomal DNA of a host cell. Such recombinantpolynucleotides typically comprise an HCV genomic or cDNA polynucleotideof semi-synthetic or synthetic origin by virtue of human manipulation.Therefore, recombinant nucleic acids comprising these sequences andcomplements thereof that are not naturally occurring are provided.

Although nucleic acids encoding NS3/4A chimeric peptides or TCEsequences or nucleic acids having sequences that complement the NS3/4Achimeric sequences or TCE sequences as they appear in nature can beemployed, they will often be altered, e.g., by deletion, substitution,or insertion, and can be accompanied by sequence not present in nature.As used herein, regulatory elements include, but are not limited to,inducible and non-inducible promoters, enhancers, operators and otherelements known to those skilled in the art that drive and regulateexpression. Such regulatory elements include, but are not limited to,the cytomegalovirus hCMV immediate early gene, the early or latepromoters of SV40 adenovirus, the lac system, the trp system, the TACsystem, the TRC system, the major operator and promoter regions of phageA, the control regions of fd coat protein, the promoter for3-phosphoglycerate kinase, the promoters of acid phosphatase, and thepromoters of the yeast-mating factors.

In addition, recombinant NS3/4A chimeric peptide-encoding nucleic acidsequences and their complementary sequences can be engineered so as tomodify their processing or expression. For example, and not by way oflimitation, the HCV nucleic acids described herein can be combined witha promoter sequence and/or ribosome binding site, or a signal sequencecan be inserted upstream of chimeric polypeptide-encoding sequences soas to permit secretion of the peptide and thereby facilitate harvestingor bioavailability. Additionally, a given NS3/4A or TCE nucleic acid canbe mutated in vitro or in vivo, to create and/or destroy translation,initiation, and/or termination sequences, or to create variations incoding regions and/or form new restriction sites or destroy preexistingones, or to facilitate further in vitro modification. (See, Examples 1and 2). Any technique for mutagenesis known in the art can be used,including but not limited to, in vitro site-directed mutagenesis.(Hutchinson et al., J. Biol. Chem., 253:6551 (1978)). The nucleic acidsencoding the chimeric NS3/4A polypeptides described above, can bemanipulated using conventional techniques in molecular biology so as tocreate recombinant constructs that express the NS3/4A recombinantpeptides.

Further, nucleic acids encoding other proteins or domains of otherproteins can be joined to nucleic acids encoding an HCV peptide so as tocreate a fusion protein. Nucleotides encoding fusion proteins caninclude, but are not limited to, a full length NS3/4A sequence (SEQ. ID.NO.: 2 or SEQ. ID. NO.: 36), mutant NS3/4A sequences (e.g., SEQ. ID.NOs.: 3-11 or 40-220) or a peptide fragment of an NS3/4A sequence fusedto an unrelated protein or peptide, such as for example, polyhistidine,hemagglutinin, an enzyme, fluorescent protein, or luminescent protein,as discussed below.

It was discovered that the construct “NS3/4A-pVAX” was significantlymore immunogenic in vivo than the construct “NS3-pVAX”. Surprisingly, itwas also discovered that the codon-optimized NS3/4A containing construct(“MSLF1-pVAX”) was more immunogenic in vivo than NS3/4A pVAX. Theexample below describes these experiments.

Example 3

To determine whether a humoral immune response was elicited by theNS3-pVAX and NS3/4A-pVAX vectors, the expression constructs described inExample 1 were purified using the Qiagen DNA purification system,according to the manufacturer's instructions and the purified DNAvectors were used to immunize groups of four to ten Balb/c mice. Theplasmids were injected directly into regenerating tibialis anterior (TA)muscles as previously described (Davis et al., Human Gene Therapy4(6):733 (1993)). In brief, mice were injected intramuscularly with 50μl/TA of 0.01 mM cardiotoxin (Latoxan, Rosans, France) in 0.9% sterileNaCl. Five days later, each TA muscle was injected with 50 μl PBScontaining either rNS3 or DNA.

Inbred mouse strains C57/BL6 (H-2b), Balb/C(H-2d), and CBA (H-2k) wereobtained from the breeding facility at Möllegard Denmark, Charles RiverUppsala, Sweden, or B&K Sollentuna Sweden. All mice were female and wereused at 4-8 weeks of age. For monitoring of humoral responses, all micereceived a booster injection of 50 μl/TA of plasmid DNA every fourthweek. In addition, some mice were given recombinant NS3 (rNS3) protein,which was purified, as described herein. The mice receiving rNS3 wereimmunized no more than twice. All mice were bled twice a month.

Enzyme immunosorbent assays (EIAs) were used to detect the presence ofmurine NS3-specific antibodies. These assays were performed essentiallyas described (Chen et al., Hepatology 28(1): 219 (1998)). Briefly, rNS3was passively adsorbed overnight at 4° C. to 96-well microtiter plates(Nunc, Copenhagen, Denmark) at 1 μg/ml in 50 mM sodium carbonate buffer(pH 9.6). The plates were then blocked by incubation with dilutionbuffer containing PBS, 2% goat serum, and 1% bovine serum albumin forone hour at 37° C. Serial dilutions of mouse sera starting at 1:60 werethen incubated on the plates for one hour. Bound murine serum antibodieswere detected by an alkaline phosphatase conjugated goat anti-mouse IgG(Sigma Cell Products, Saint Louis, Mo.) followed by addition of thesubstrate pNPP (1 tablet/5 ml of 1M Diethanol amine buffer with 0.5 mMMgCl₂). The reaction was stopped by addition of 1M NaOH and absorbencywas read at 405 nm.

After four weeks, four out of five mice immunized with NS3/4A-pVAX haddeveloped NS3 antibodies, whereas one out of five immunized withNS3-pVAX had developed antibodies (FIG. 2). After six weeks, four out offive mice immunized with NS3/4A-pVAX had developed high levels (>10⁴) ofNS3 antibodies (mean levels 10800±4830) and one had a titer of 2160.Although all mice immunized with NS3-pVAX developed NS3 antibodies, noneof them developed levels as high as that produced by the NS3/4A-pVAXconstruct (mean levels 1800±805). The antibody levels elicited by theNS3/4A fusion construct were significantly higher than those induced byNS3-pVAX at six weeks (mean ranks 7.6 vs. 3.4, p<0.05, Mann-Whitney ranksum test, and p<0.01, Students t-test). Thus, immunization with eitherNS3-pVAX or NS3/4A-pVAX resulted in the production of NS3-specificantibodies, but the NS3/4A containing construct was a more potentimmunogen.

A similar experiment was conducted to compare the immunogenicity of theNS3/4A-pVAX and MSLF1-pVAX constructs. To better resemble a futurevaccination schedule in humans, however, the plasmids were delivered togroups of ten mice using a gene gun. In brief, plasmid DNA was linked togold particles according to protocols supplied by the manufacturer(Bio-Rad Laboratories, Hercules, Calif.). Prior to immunization, theinjection area was shaved and the immunization was performed accordingto the manufacturer's protocol. Each injection dose contained 4 μg ofplasmid DNA. Immunizations were performed on weeks 0, 4, and 8.

The MSLF1 gene was found to be more immunogenic than the native NS3/4Agene since NS3-specific antibodies were significantly higher in miceimmunized with the MSLF1-pVAX construct at two weeks after the secondand third immunization (TABLE 5). These results confirmed that thecodon-optimized MSLF1-pVAX was a more potent B cell immunogen thanNS3/4A-pVAX.

TABLE 5 No. of Mean Immunogen Week injections NS3 titre SD Mann-WhitneyNS3/4A 2 1 0 0 NS MSLF1 2 1 0 0 NS3/4A 6 2 0 0 p < 0.0002 MSLF1 6 2 24843800 NS3/4A 10 3 60 0 p < 0.0001 MSLF1 10 3 4140 4682

The example below provides more evidence that MSLF-1 (coNS3/4a) producesa strong humoral response.

Example 3A

To test the intrinsic immunogenicity of the different NS3 genes groupsof BALB/c (H-2^(d)) mice were immunized with the following vectors:wtNS3/4A (wild type NS3/4a), coNS3/4A (codon-optimized NS3/4a orMSLF-1), or wtNS3/4A-SFV (wild-type NS3/4A obtained from SFVexpression). Doses of 4 μg DNA was administered using the gene gun anddoses of 10⁷ SFV particles were injected subcutaneously (s.c.). The micewere boosted after four weeks. The mice immunized with the wtNS3/4A-SFVdeveloped antibodies already after the first injection suggesting apotent immunogenicity (FIGS. 3A and 3B). At two weeks after the secondimmunization most mice immunized with the coNS3/4A or wtNS3/4A-SFVvectors had developed mean antibody levels over 10³ (FIGS. 3A and 3B).In contrast, none of the mice immunized with the wtNS3/4A plasmid haddeveloped detectable NS3-specific antibodies at six weeks (FIGS. 3A and3B). Thus, both codon optimization and mRNA amplification by SFV resultsin an increased B cell immunogenicity of the NS3/4A gene.

To indirectly compare the T helper 1 (Th1) and Th2-skewing of the T cellresponse primed by wtNS3/4A, coNS3/4A, and wtNS3/4A-SFV immunizationsthe levels of NS3-specific IgG1 (Th2) and IgG2a (Th1) antibodies wereanalyzed (FIGS. 3A and 3B). The IgG2a/IgG1-ratio in mice immunized withrNS3 with or without adjuvant was always <1 regardless of the murinehaplotype, signaling a Th2-dominated response. In contrast, miceimmunized i.m. with the wtNS3 (wild-type NS3), wtNS3/4A, or coNS3/4Acontaining plasmids had Th1-skewed Th-cell responses evidenced byIgG2a/IgG1 ratios of >1 (FIG. 3B). Thus, codon optimization did notchange the IgG subclass distribution. When genetically immunizing BALB/cmice with NS3/4A using the gene gun the subclass ratio suggested a mixedTh1/Th2 response (FIG. 3B). It should be noted that the codon optimizedplasmid did not display an increased in vitro stimulatory capacity of Bcells, as compared to the native plasmid, suggesting that no majorimmune stimulatory motifs had been lost or introduced.

Immunizations using SFV primed a Th1-, or mixed Th1/Th2-like isotypedistribution. The anti-NS3 IgG2a/IgG1-ratio following wtNS3/4A-SFVimmunization ranged from 2.4 to 20 between different experimentsproviding evidence of a Th1-like response. This is similar to theprevious experience with SFV vectors where a Th1-skewed IgG subclassdistribution was observed.

The example below describes experiments that were performed to determineif mutant NS3/4A peptides, which lack a proteolytic cleavage site, couldelicit an immune response to NS3.

Example 4

To test if the enhanced immunogenicity of NS3/4A could be solelyattributed to the presence of NS4A, or if the NS3/4A fusion protein inaddition had to be cleaved at the NS3/4A junction, another set ofexperiments were performed. In a first experiment, the immunogenicity ofthe NS3-pVAX, NS3/4A-pVAX, and mutant NS3/4A constructs were compared inBalb/c mice. Mice were immunized on week 0 as described above, and,after two weeks, all mice were bled and the presence of antibodies toNS3 at a serum dilution of 1:60 was determined (TABLE 6). Mice were bledagain on week 4. As shown in TABLE 6, all the constructs induced animmune response; the mutant constructs, for example, the NS3/4A-TGT-pVAXvector was comparable to the NS3-pVAX vector (4/10 vs. 0/10; NS,Fisher's exact test). The NS3/4A-pVAX vector, however, was more potentthan the mutant constructs.

TABLE 6 No. of antibody responders to the respective immunogen after one100 μg i.m immunization Weeks from 1^(st) wild-type mutant exampleimmunization NS3-pVAX NS3/4A-pVAX NS3/4A-TGT-pVAX 2 0/10 17/20  4/10 40/10 20/20 10/10 (<60) (2415 ± 3715) (390 ± 639) 55% > 10³ 50% > 10²10% > 10⁴ 10% > 10³

During the chronic phase of infection, HCV replicates in hepatocytes,and spreads within the liver. A major factor in combating chronic andpersistent viral infections is the cell-mediated immune defense system.CD4+ and CD8+ lymphocytes infiltrate the liver during the chronic phaseof HCV infection, but they are incapable of clearing the virus orpreventing liver damage. In addition, persistent HCV infection isassociated with the onset of hepatocellular carcinoma (HCC). Theexamples below describe experiments that were performed to determinewhether the NS3, NS3/4A, and MSLF1 constructs were capable of elicitinga T-cell mediated immune response against NS3.

Example 5

To study whether the constructs described above were capable ofeliciting a cell-mediated response against NS3, an in vivo tumor growthassay was performed. To this end, an SP2/0 tumor cell line (SP2/0-Ag14myeloma cell line (H-2^(d))) stably transfected with the NS3/4A gene wasmade. The SP2/0 cells were maintained in DMEM medium supplemented with10% fetal calf serum (FCS; Sigma Chemicals, St. Louis, Mo.), 2 mML-Glutamine, 10 mM HEPES, 100 U/ml Penicillin and 100 μg/mlStreptomycin, 1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 1mM sodium pyruvate (GIBCO-BRL, Gaithesburgh, Md.). The pcDNA3.1 plasmidcontaining the NS3/4A gene was linearized by BglII digestion. A total of5 μg linearized plasmid DNA was mixed with 60 μg transfection reagent(Superfect, Qiagen, Germany) and the mixture was added to a 50%confluent layer of SP2/0 cells in a 35 mm dish. The transfectionprocedure was performed according to manufacturer's protocol.

Transfected cells were cloned by limiting dilution and selected byaddition of 800 μg geneticin (G418)/ml complete DMEM medium after 14days. A stable NS3/4A-expressing SP2/0 clone was identified using PCRand RTPCR and/or a capture EIA using a monoclonal antibody to NS3. AllEIAs for the detection of murine NS3 antibodies were essentiallyperformed as follows. In brief, rNS3 (recombinant NS3 protein producedin E. Coli, dialyzed overnight against PBS, and sterile filtered) waspassively adsorbed overnight at 4° C. to 96-well microtiter plates(Nunc, Copenhagen, Denmark) at 1 μg/ml in 50 mM sodium carbonate buffer(pH 9.6). The plates were then blocked by incubation with dilutionbuffer containing PBS, 2% goat serum, and 1% bovine serum albumin forone hour at +37° C. Serial dilutions of mouse sera starting at 1:60 werethen incubated on the plates for one hour. Bound murine serum antibodieswere detected by an alkaline phosphatase conjugated goat anti-mouse IgG(Sigma cellproducts, Saint Louis, Mo. USA) followed by addition of thesubstrate pNPP (1 tablet/5 ml of 1M Diethanolamine buffer with 0.5 mMMgCl2). The reaction was stopped by addition of 1M NaOH. Absorbance wasthen read at 405 nm.

The in vivo growth kinetics of the SP2/0 and the NS3/4A-SP2/0 cell lineswere then evaluated in Balb/c mice. Mice were injected subcutaneouslywith 2×10⁶ tumor cells in the right flank. Each day the size of thetumor was determined through the skin. The growth kinetics of the twocell lines was comparable. The mean tumor sizes did not differ betweenthe two cell lines at any time point, for example. (See TABLE 7).

TABLE 7 Mouse Tumor Maximum in vivo tumor size at indicated time pointID cell line 5 6 7 8 11 12 13 14 15 1 SP2/0 1.6 2.5 4.5 6.0 10.0 10.511.0 12.0 12.0 2 SP2/0 1.0 1.0 2.0 3.0 7.5 7.5 8.0 11.5 11.5 3 SP2/0 2.05.0 7.5 8.0 11.0 11.5 12.0 12.0 13.0 4 SP2/0 4.0 7.0 8.0 10.0 13.0 15.016.5 16.5 17.0 5 SP2/0 1.0 1.0 3.0 4.0 5.0 6.0 6.0 6.0 7.0 Group mean1.92 3.3 5.0 6.2 9.3 10.1 10.7 11.6 12.1 6 NS3/4A-SP2/0 1.0 2.0 3.0 3.54.0 5.5 6.0 7.0 8.0 7 NS3/4A-SP2/0 2.0 2.5 3.0 5.0 7.0 9.0 9.5 9.5 11.08 NS3/4A-SP2/0 1.0 2.0 3.5 3.5 9.5 11.0 12.0 14.0 14.0 9 NS3/4A-SP2/01.0 1.0 2.0 6.0 11.5 13.0 14.5 16.0 18.0 10 NS3/4A-SP2/0 3.5 6.0 7.010.5 15.0 15.0 15.0 15.5 20.0 Group mean 1.7 2.7 3.7 5.7 9.4 10.7 11.412.4 14.2 p-value of student's 0.7736 0.6918 0.4027 0.7903 0.9670 0.79860.7927 0.7508 0.4623 t-test comparison between group means

The example below describes experiments that were performed to determinewhether mice immunized with the NS3/4A constructs had developed a T-cellresponse against NS3.

Example 6

To examine whether a T-cell response was elicited by the NS3/4Aimmunization, the capacity of an immunized mouse's immune defense systemto attack the NS3-expressing tumor cell line was assayed. The protocolfor testing for in vivo inhibition of tumor growth of the SP2/0 myelomacell line in Balb/c mice has been described in detail previously (Enckeet al., J. Immunol. 161:4917 (1998)). Inhibition of tumor growth in thismodel is dependent on the priming of cytotoxic T lymphocytes (CTLs). Ina first set of experiments, groups of ten mice were immunized i.m. fivetimes with one month intervals with either 100 μg NS3-pVAX or 100 μgNS3/4A-pVAX. Two weeks after the last immunization 2×10⁶ SP2/0 orNS3/4A-SP2/0 cells were injected into the right flank of each mouse. Twoweeks later the mice were sacrificed and the maximum tumor sizes weremeasured. There was no difference between the mean SP2/0 andNS3/4A-SP2/0 tumor sizes in the NS3-pVAX immunized mice. (See TABLE 8).

TABLE 8 Maximum Dose Tumor tumor size Mouse ID Immunogen (μg) Tumor cellline growth (mm) 1 NS3-pVAX 100 SP2/0 Yes 5 2 NS3-pVAX 100 SP2/0 Yes 153 NS3-pVAX 100 SP2/0 No — 4 NS3-pVAX 100 SP2/0 Yes 6 5 NS3-pVAX 100SP2/0 Yes 13 Group total 4/5 9.75 ± 4.992 6 NS3-pVAX 100 NS3/4A-SP2/0Yes 9 7 NS3-pVAX 100 NS3/4A-SP2/0 Yes 8 8 NS3-pVAX 100 NS3/4A-SP2/0 Yes7 9 NS3-pVAX 100 NS3/4A-SP2/0 No — 10  NS3-pVAX 100 NS3/4A-SP2/0 No —3/5 8.00 ± 1.00  Note: Statistical analysis (StatView): Student's t-teston maximum tumor size. P-values < 0.05 are considered significant.Unpaired t-test for Max diam Grouping Variable: Column 1 HypothesizedDifference = 0 Row exclusion: NS3DNA-Tumor-001213 Mean Diff. DF t-ValueP-Value NS3-sp2, NS3-spNS3 1.750 5 0.58 0.584 Group Info for Max diamGrouping Variable: Column 1 Row exclusion: NS3DNA-Tumor-001213 CountMean Variance Std. Dev. Std. Err NS3-sp2 4 9.750 24.917 4.992 2.496NS3-spNS3 3 8.000  1.000 1.000 0.57

To analyze whether administration of different NS3 containingcompositions affected the elicitation of a cell-mediated immuneresponse, mice were immunized with PBS, rNS3, a control DNA, or theNS3/4A construct, and tumor sizes were determined, as described above.The NS3/4A construct was able to elicit a T-cell response sufficient tocause a statistically significant reduction in tumor size (See TABLE 9).

TABLE 9 Maximum Mouse Dose Tumor Tumor tumor size ID Immunogen (μg) cellline Anti-NS3 growth (mm) 1 NS3-pVAX 10 NS3/4A-SP2/0 <60 + 12.0 2NS3-pVAX 10 NS3/4A-SP2/0 <60 + 20.0 3 NS3-pVAX 10 NS3/4A-SP2/0 60 + 18.04 NS3-pVAX 10 NS3/4A-SP2/0 <60 + 13.0 5 NS3-pVAX 10 NS3/4A-SP2/0 <60 +17.0 Group mean 60 5/5  16.0 ± 3.391 6 NS3-pVAX 100 NS3/4A-SP2/0 2160 +10.0 7 NS3-pVAX 100 NS3/4A-SP2/0 <60 − — 8 NS3-pVAX 100 NS3/4A-SP2/0 <60− — 9 NS3-pVAX 100 NS3/4A-SP2/0 360 − — 10 NS3-pVAX 100 NS3/4A-SP2/0<60 + 12.5 Group mean 1260 2/5 11.25 ± 1.768 11 NS3/4A-pVAX 10NS3/4A-SP2/0 <60 + 10.0 12 NS3/4A-pVAX 10 NS3/4A-SP2/0 <60 − — 13NS3/4A-pVAX 10 NS3/4A-SP2/0 <60 − — 14 NS3/4A-pVAX 10 NS3/4A-SP2/0 <60 +13.0 15 NS3/4A-pVAX 10 NS3/4A-SP2/0 <60 + 13.5 Group mean <60 3/5 12.167± 1.893  16 NS3/4A-pVAX 100 NS3/4A-SP2/0 60 + 10.0 17 NS3/4A-pVAX 100NS3/4A-SP2/0 360 − — 18 NS3/4A-pVAX 100 NS3/4A-SP2/0 2160 + 8.0 19NS3/4A-pVAX 100 NS3/4A-SP2/0 2160 + 12.0 20 NS3/4A-pVAX 100 NS3/4A-SP2/02160 + 7.0 Group mean 1380 4/5  9.25 ± 2.217 36 p17-pcDNA3 100NS3/4A-SP2/0 <60 + 20.0 37 p17-pcDNA3 100 NS3/4A-SP2/0 <60 + 7.0 38p17-pcDNA3 100 NS3/4A-SP2/0 <60 + 11.0 39 p17-pcDNA3 100 NS3/4A-SP2/0<60 + 15.0 40 p17-pcDNA3 100 NS3/4A-SP2/0 <60 + 18.0 Group mean <60 5/514.20 ± 5.263 41 rNS3/CFA 20 NS3/4A-SP2/0 >466560 + 13.0 42 rNS3/CFA 20NS3/4A-SP2/0 >466560 − — 43 rNS3/CFA 20 NS3/4A-SP2/0 >466560 + 3.5 44rNS3/CFA 20 NS3/4A-SP2/0 >466560 + 22.0 45 rNS3/CFA 20NS3/4A-SP2/0 >466560 + 17.0 Group mean 466560 4/5 17.333 ± 4.509  46 PBS— NS3/4A-SP2/0 <60 + 10.0 47 PBS — NS3/4A-SP2/0 <60 + 16.5 48 PBS —NS3/4A-SP2/0 60 + 15.0 49 PBS — NS3/4A-SP2/0 <60 + 21.0 50 PBS —NS3/4A-SP2/0 <60 + 15.0 51 PBS — NS3/4A-SP2/0 <60 − — Group mean 60 5/615.50 ± 3.937 Unpaired t-test for Largest Tumor size Grouping Variable:group Hypothesized Difference = 0 Mean Diff. DF t-Value P-Valuep17-sp3-4, NS3-100-sp3-4 2.950 5 .739 .4933 p17-sp3-4, NS3/4-10-sp3-42.033 6 .628 .5532 p17-sp3-4, NS3-10-sp3-4 −1.800 8 −.643 .5383p17-sp3-4, NS3/4-100-sp3-4 4.950 7 1.742 .1250 p17-sp3-4, PBS-sp3-4−1.300 8 −.442 .6700 p17-sp3-4, rNS3-sp3-4 −3.133 6 −.854 .4259NS3-100-sp3-4, NS3/4-10-sp3-4 −.917 3 −.542 .6254 NS3-100-sp3-4,NS3-10-sp3-4 −4.750 5 −1.811 .1299 NS3-100-sp3-4, NS3/4-100-sp3-4 2.0004 1.092 .3360 NS3-100-sp3-4, PBS-sp3-4 −4.250 5 −1.408 .2183NS3-100-sp3-4, rNS3-sp3-4 −6.083 3 −1.744 .1795 NS3/4-10-sp3-4,NS3-10-sp3-4 −3.833 6 −1.763 .1283 NS3/4-10-sp3-4, NS3/4-100-sp3-4 2.9175 1.824 .1277 NS3/4-10-sp3-4, PBS-sp3-4 −3.333 6 −1.344 .2274NS3/4-10-sp3-4, rNS3-sp3-4 −5.167 4 −1.830 .1412 NS3-10-sp3-4,NS3/4-100-sp3-4 6.750 7 3.416 .0112 NS3-10-sp3-4, PBS-sp3-4 .500 8 .215.8350 NS3-10-sp3-4, rNS3-sp3-4 −1.333 6 −.480 .6480 NS3/4-100-sp3-4,PBS-sp3-4 −6.250 7 −2.814 .0260 NS3/4-100-sp3-4, rNS3-sp3-4 −8.083 5−3.179 .0246 PBS-sp3-4, rNS3-sp3-4 −1.833 6 −.607 .5662 Note:Statistical analysis (StatView): Student's t-test on maximum tumor size.P-values <0.05 are considered as significant.

The example below describes more experiments that were performed todetermine whether the reduction in tumor size can be attributed to thegeneration of NS3-specific T-lymphocytes.

Example 7

In the next set of experiments, the inhibition of SP2/0 or NS3/4A-SP2/0tumor growth was again evaluated in NS3/4A-pVAX immunized Balb/c mice.In mice immunized with the NS3/4A-pVAX plasmid, the growth ofNS3/4A-SP2/0 tumor cells was significantly inhibited as compared togrowth of the non-transfected SP2/0 cells. (See TABLE 10). Thus,NS3/4A-pVAX immunization elicits CTLs that inhibit growth of cellsexpressing NS3/4A in vivo.

TABLE 10 Maximum Dose Tumor Tumor tumor size Mouse ID Immunogen (μg)cell line growth (mm) 11 NS3/4A-pVAX 100 SP2/0 No — 12 NS3/4A-pVAX 100SP2/0 Yes 24 13 NS3/4A-pVAX 100 SP2/0 Yes 9 14 NS3/4A-pVAX 100 SP2/0 Yes11 15 NS3/4A-pVAX 100 SP2/0 Yes 25 4/5 17.25 ± 8.421 16 NS3/4A-pVAX 100NS3/4A- No — SP2/0 17 NS3/4A-pVAX 100 NS3/4A- Yes 9 SP2/0 18 NS3/4A-pVAX100 NS3/4A- Yes 7 SP2/0 19 NS3/4A-pVAX 100 NS3/4A- Yes 5 SP2/0 20NS3/4A-pVAX 100 NS3/4A- Yes 4 SP2/0 4/5  6.25 ± 2.217 Note: Statisticalanalysis (StatView): Student's t-test on maximum tumor size. P-values <0.05 are considered significant. Unpaired t-test for Max diam GroupingVariable: Column 1 Hypothesized Difference = 0 Row exclusion:NS3DNA-Tumor-001213 Mean Diff. DF t-Value P-Value NS3/4-sp2, NS3/4-spNS311.000 6 2.526 0.044 Group Info for Max diam Grouping Variable: Column 1Row exclusion: NS3DNA-Tumor-001213 Count Mean Variance Std. Dev. Std.Err NS3/4-sp2 4 17.250 70.917 8.421 4.211 NS3/4-spNS3 4  6.250  4.9172.217 1.109

In another set of experiments, the inhibition of NS3/4A-expressing SP2/0tumor growth was evaluated in MSLF1-pVAX immunized Balb/c mice. Inbrief, groups of mice were immunized with different immunogens (4 μg ofplasmid) using a gene gun at weeks zero, four, eight, twelve, andsixteen. Two weeks after the last immunization approximately 2×10⁶NS3/4A-expressing SP2/0 cells were injected s.c. into the right flank ofthe mouse. The kinetics of the tumor growth was then monitored bymeasuring the tumor size through the skin at days seven, 11, and 13. Themean tumor sizes were calculated and groups were compared using theMann-Whitney non-parametric test. At day 14 all mice were sacrificed.

After only a single immunization, tumor inhibiting responses wereobserved. (See FIG. 3 and TABLE 11). After two immunizations, both theNS3/4A-pVAX and MSLF1-pVAX plasmids primed tumor-inhibiting responses.(See FIG. 4A and TABLE 12). The tumors were significantly smaller inmice immunized with the MSLF1 gene, however, as compared to the nativeNS3/4A gene. After three injections, both plasmids effectively primedcomparable tumor inhibiting responses. (See FIG. 4B and TABLE 13). Theseexperiments provided evidence that the MSLF-1 gene was more efficient inactivating tumor inhibiting immune responses in vivo than NS3/4A-pVAX.

TABLE 11 MSLF1- Group pVAX1 NS3/4A-pVAX1 Non-immunized MSLF1-pVAX1 —N.S. p < 0.05 NS3/4A-pVAX1 N.S. — p < 0.05 Non-immunized p < 0.05 p <0.05 —

TABLE 12 MSLF1- Group pVAX1 NS3/4A-pVAX1 Non-immunized MSLF1-pVAX1 — p <0.05 p < 0.01 NS3/4A-pVAX1 p < 0.05 — p < 0.01 Non-immunized p < 0.01 p< 0.01 —

TABLE 13 MSLF1- Group pVAX1 NS3/4A-pVAX1 Non-immunized MSLF1-pVAX1 —N.S. p < 0.01 NS3/4A-pVAX1 N.S. — p < 0.01 Non-immunized p < 0.01 p <0.01 —

The example below describes experiments that were performed to analyzethe efficiency of various NS3 containing compositions in eliciting acell-mediated response to NS3.

Example 8

To determine whether NS3-specific T-cells were elicited by the NS3/4Aimmunizations, an in vitro T-cell mediated tumor cell lysis assay wasemployed. The assay has been described in detail previously (Sallberg etal., J. Virol. 71:5295 (1997)). In a first set of experiments, groups offive Balb/c mice were immunized three times with 100 μg NS3/4A-pVAX i.m.Two weeks after the last injection the mice were sacrificed andsplenocytes were harvested. Re-stimulation cultures with 3×10⁶splenocytes and 3×10⁶ NS3/4A-SP2/0 cells were set. After five days, astandard Cr⁵¹-release assay was performed using NS3/4A-SP2/0 or SP2/0cells as targets. Percent specific lysis was calculated as the ratiobetween lysis of NS3/4A-SP2/0 cells and lysis of SP2/0 cells. Miceimmunized with NS3/4A-pVAX displayed specific lysis over 10% in four outof five tested mice, using an effector to target ratio of 20:1 (SeeFIGS. 6A and 6B).

In a next set of experiments, the T cell responses to MSLF1-pVAX andNS3/4A-pVAX were compared. The ability of the two plasmids to prime invitro detectable CTLs were evaluated in C57/BL6 mice since anH-2b-restricted NS3 epitope had been previously mapped. Groups of micewere immunized with the two plasmids and CTLs were detected in vitrousing either peptide coated H-2b expressing RMA-S cells orNS3/4A-expressing EL-4 cells. Briefly, in vitro stimulation was carriedout for five days in 25-ml flasks at a final volume of 12 ml, containing5 U/ml recombinant murine IL-2 (mIL-2; R&D Systems, Minneapolis, Minn.).The restimulation culture contained a total of 40×10⁶ immune spleencells and 2×10⁶ irradiated (10,000 rad) syngenic SP2/0 cells expressingthe NS3/4A protein. After five days in vitro stimulation a standard⁵¹Cr-release assay was performed. Effector cells were harvested and afour-hour ⁵¹Cr assay was performed in 96-well U-bottom plates in a totalvolume of 200 μl. A total of 1×10⁶ target cells was labeled for one hourwith 20 μl of ⁵¹Cr (5 mCi/ml) and then washed three times in PBS.Cytotoxic activity was determined at effector:target (E:T) ratios of40:1, 20:1, and 10:1, using 5×10³ ⁵¹Cr-labeled target cells/well.

Alternatively, splenocytes were harvested from C57BL/6 mice 12 daysafter peptide immunization and were resuspended in RPMI 1640 mediumsupplemented with 10% FCS, 2 mM L-Glutamine, 10 mM HEPES, 100 U/mlPenicillin and 100 μg/ml Streptomycin, 1 mM non-essential amino acids,50 μM β-mercaptoethanol, 1 mM sodium pyruvate. In vitro stimulation wascarried out for five days in 25 ml flasks in a total volume of 12 ml,containing 25×10⁶ spleen cells and 25×10⁶ irradiated (2,000 rad)syngeneic splenocytes. The restimulation was performed in the presenceof 0.05 μM NS3/4A H-2D^(b) binding peptide (sequence GAVQNEVTL SEQ. ID.NO.: 37) or a control peptide H-2D^(b) peptide (sequence KAVYNFATM SEQ.ID. NO.: 38). After five days a ⁵¹Cr-release assay was performed. RMA-Starget cells were pulsed with 50 μM peptide for 1.5 hrs at +37° C. priorto ⁵¹Cr-labelling, and then washed three times in PBS. Effector cellswere harvested and the four hour ⁵¹Cr assay was performed as described.Cytotoxic activity was determined at the E:T ratios 60:1, 20:1, and 7:1with 5×10³ ⁵¹Cr-labeled target cells/well. By these assays, it wasdetermined that the MSLF1 gene primed higher levels of in vitro lyticactivity compared to the NS3/4A-pVAX vector. (See FIG. 7A-7L). Similarresults were obtained with both the peptide coated H-2b expressing RMA-Scells and NS3/4A-expressing EL-4 cells.

Additional evidence that the codon-optimized MSLF1 gene primedNS3-specific CTLs more effectively than the native NS3/4A gene wasobtained using flow cytometry. The frequency of NS3/4A-peptide specificCD8+ T cells were analyzed by ex-vivo staining of spleen cells fromNS3/4A DNA immunized mice with recombinant soluble dimeric mouseH-2D^(b):Ig fusion protein. Many of the monoclonal antibodies and MHC:Igfusion proteins described herein were purchased from BDB Pharmingen (SanDiego, Calif.); Anti-CD16/CD32 (Fc-Block™, clone 2.4G2), FITC conjugatedanti-CD8 (clone 53-6.7), FITC conjugated anti-H-2K^(b) (clone AF6-88.5),FITC conjugated anti-H-2D^(b) (clone KH95), recombinant soluble dimericmouse H-2D^(b):Ig, PE conjugated Rat-α Mouse IgG1 (clone X56).

Approximately, 2×10⁶ spleen cells resuspended in 100 μl PBS/1% FCS (FACSbuffer) were incubated with 1 μg/10⁶ cells of Fc-blocking antibodies onice for 15 minutes. The cells were then incubated on ice for 1.5 hrswith either 2 μg/10⁶ cells of H-2D^(b):Ig preloaded for 48 hours at +4°C. with 640 nM excess of NS3/4A derived peptide (sequence GAVQNEVTL SEQ.ID. NO.: 37) or 2 μg/10⁶ cells of unloaded H-2D^(b):Ig fusion protein.The cells were then washed twice in FACS buffer and resuspended in 100μl FACS buffer containing 10 μg/100 μl PE conjugated Rat-α Mouse IgG1secondary antibody and incubated on ice for 30 minutes. The cells werethen washed twice in FACS buffer and incubated with 1 μg/10⁶ cells ofFITC conjugated α-mouse CD8 antibody for 30 minutes. The cells were thenwashed twice in FACS buffer and resuspended in 0.5 ml FACS buffercontaining 0.5 μg/ml of PI. Approximately 200,000 events from eachsample were acquired on a FACS Calibur (BDB) and dead cells (PI positivecells) were excluded from the analysis.

The advantage of quantifying specific CTLs by FACS analysis is that itbypasses the possible disadvantages of in vitro expansion of CTLs invitro prior to analysis. Direct ex-vivo quantification of NS3-specificCTLs using NS3-peptide loaded divalent H-2D^(b):Ig fusion proteinmolecules revealed that the codon optimized MSLF-1 gene primed aeffectively primed NS3-specific CTLs already after two immunizations,whereas the original NS3/4A gene did not. Thus, the optimized MSLF-1gene effectively primes NS3-specific CTLs that are of higher frequencyand of better functionality by all parameters tested, as compared to theoriginal NS3/4A gene. The example below provides more evidence thatcodon optimized NS3/4A efficiently primes NS3 specific cytotoxic Tcells.

Example 8A

Initially, the frequency of NS3-specific CTLs that could be primed bygene gun immunization using the wtNS3, wtNS3/4A and coNS3/4A expressingplasmids was determined. The coNS3/4A plasmid primed higher precursorfrequencies of NS3-specific CTL as compared to the wtNS3 gene enforcingthe importance of NS4A (FIG. 8A). No statistical difference in CTLprecursor frequencies was noted between the wtNS3/4A and coNS3/4Aexpressing plasmids when analyzed directly ex vivo (FIG. 8A). A singleimmunization with the coNS3/4A plasmid or wtNS3/4A-SFV primed around 1%of peptide-specific CTLs within two weeks from immunization (FIG. 8A).The specificity of the detection of NS3-specific CTLs was confirmed by afive-day restimulation in vitro with the NS3-peptide, by which highprecursor frequencies were observed after immunization with the coNS3/4Agene (FIG. 8A).

To directly compare the in vitro lytic activity of the NS3-specific CTLsprimed by different vectors, a standard ⁵¹Cr-release assay was performedafter one or two immunizations. The lytic activity of the in vivo primedCTLs were assayed on both NS3-peptide loaded H-2D^(b) expressing RMA-Scells and EL-4 cells stably expressing NS3/4A. After one dose, thecoNS3/4A plasmid and the wtNS3/4A-SFV vector was clearly more efficientthan the wtNS3/4A plasmid in priming CTLs that lysed NS3-peptide coatedtarget cells (FIGS. 9A and 9B). Thus, the CTL priming event was enhancedby codon optimization or mRNA amplification of the NS3/4A gene. Thedifference was less clear when using the NS3/4A-expressing EL-4 cellspresumably since this assay is less sensitive (FIGS. 9A and 9B). Aftertwo immunizations all NS3/4A vectors seemed to prime NS3-specific CTLswith a similar efficiency (FIG. 9B). However, two immunizations with anyof the NS3/4A-containing vectors were clearly more efficient in primingNS3-specific CTLs as compared to the plasmid containing only the wtNS3gene (FIG. 9B), which is fully consistent with the CTL precursoranalysis and previous observations. Thus, codon optimization or mRNAamplification of the NS3/4A gene more rapidly primes NS3-specific CTLs.

Analysis of the inhibition of tumor growth in vivo in BALB/c mice usingSP2/0 myeloma cells, or in C57BL/6 mice using EL-4 lymphoma cells,expressing an HCV viral antigen is recognized by those in the field torepresent the in vivo functional HCV-specific immune response. (SeeEncke J et al., J Immunol 161: 4917-4923 (1998)). An SP2/0 cell linestably expressing NS3/4A has previously been described (see Frelin L etal., Gene Ther 10: 686-699 (2003)) and an NS3/4A expressing EL-4 cellline was characterized as described below.

To confirm that inhibition of tumor growth using the NS3/4A-expressingEL-4 cell line is fully dependent on an NS3/4A-specific immune responsea control experiment was performed. Groups of ten C57BL/6 mice wereeither left nonimmunized, or immunized twice with the coNS3/4A plasmid.Two weeks after the last immunization the mice were challenged with ans.c. injection of 10⁶ native EL-4 or NS3/4A-expressing EL-4 cells(NS3/4A-EL-4). An NS3/4A-specific immune response was required forprotection, since only the immunized mice were protected against growthof the NS3/4A-EL-4 cell line (FIG. 10A). Thus, this H-2^(b)-restrictedmodel behaves similarly to the SP2/0 H-2^(d) restricted model.

Immunizations with recombinant NS3 protein provided evidence that bothNS3/4A-specific B cells and CD4+ T cells were not of a pivotalimportance in protection against tumor growth. In vitro depletion ofCD4+ or CD8+ T cells of splenocytes from coNS3/4A plasmid immunizedH-2^(b) mice provided evidence that CD8+ T cells were the major effectorcells in the ⁵¹Cr-release assay. To define the in vivo functionalanti-tumor effector cell population, CD4+ or CD8+ T cells in miceimmunized with the coNS3/4A plasmid one week prior to, and during,challenge with the NS3/4A-EL-4 tumor cell line were selectivelydepleted. Analysis by flow cytometry revealed that 85% of CD4+ and CD8+T cells had been depleted, respectively. This experiment revealed thatin vivo depletion of CD4+ T cells had no significant effect on the tumorimmunity (FIG. 10B). In contrast, depletion of CD8+ T cells in vivosignificantly reduced the tumor immunity (p<0.05, ANOVA; FIG. 10B).Thus, as expected, NS3/4A-specific CD8+ CTLs seems to be the majorprotective cell at the effector stage in the in vivo model forinhibition of tumor growth.

The tumor challenge model was then used to evaluate how effective thedifferent immunogens were in priming a protective immunity againstgrowth of NS3/4A-EL-4 tumor cells in vivo. To ensure that theeffectiveness of the priming event was studied, all mice were immunizedonly once. Fully consistent with the in vitro CTL data did we find thatonly vectors containing NS3/4A were able to rapidly prime protectiveimmune responses as compared to the immunized with the empty pVAXplasmid (p<0.05, ANOVA; FIG. 11). However, this was dependent on NS4Abut independent of either codon optimization or mRNA amplification,suggesting that C57BL/6 mice are quite easily protected against tumorgrowth using genetic immunization.

To further clarify the prerequisites for priming of the in vivoprotective CD8+ CTL responses additional experiments were performed.First, C57BL/6 mice immunized with the NS3-derived CTL peptide were notprotected against growth of NS3/4A-EL-4 tumors (FIG. 11). Second,immunization with recombinant NS3 in adjuvant did not protect againsttumor growth (FIG. 11). NS3-derived CTL peptide effectively primes CTLsin C57BL/6 mice and rNS3 in adjuvant primes high levels of NS3-specificT helper cells. Thus, an endogenous production of NS3/4A seems to beneeded to prime in vivo protective CTLs. To further characterize thepriming event, groups of B cell (μMT) or CD4 deficient C57BL/6 mice wereimmunized once with the coNS3/4A gene using gene gun, and werechallenged two weeks later (FIG. 11). Since both lineages were protectedagainst tumor growth we conclude that neither B cells nor CD4+ T cellswere required for the priming of in vivo functional NS3/4A-specific CTLs(FIG. 11). In conclusion, the priming of in vivo tumor protectiveNS3/4A-specific CTLs in C57BL/6 mice requires NS4A and an endogenousexpression of the immunogen. In C57BL/6 mice the priming is lessdependent on the gene delivery route or accessory cells, such as B cellsor CD4+ T cells. The fact that the priming of in vivo functional CTL bythe coNS3/4A DNA plasmid was independent of CD4+ T helper cells may helpto explain the speed by which the priming occurred.

Repeated experiments in C57BL/6 mice using the NS3/4A-EL-4 cell linehave shown that protection against tumor growth is obtained alreadyafter the first immunization with the NS3/4A gene, independent of codonoptimization or mRNA amplification. Also, after two injections theimmunity against NS3/4A-EL-4 tumor growth was even further enhanced, butonly when NS4A was present. Thus, this model may therefore not besufficiently sensitive to reveal subtle differences in the intrinsicimmunogenicity of different immunogens.

To better compare the immunogenicity of the wtNS3/4A and the coNS3/4ADNA plasmids, additional experiments were performed in H-2^(d) mice,were at least two immunizations seemed to be required for a tumorprotective immunity. It is important to remember that the IgG subclassdistribution obtained after gene gun immunization with the NS3/4A genein BALB/c mice suggested a mixed Th1/Th2-like response. Thus, it waspossible that a Th2-like immunization route (gene gun) in the Th2-proneBALB/c mouse strain may impair the ability to prime in vivo effectiveCTL responses.

Groups of ten BALB/c mice were immunized once, twice, or thrice with 4μg of the respective DNA plasmid using the gene gun (FIGS. 12A-12C). Themice were challenged two weeks after the last injection. Accordingly,these experiments provided more evidence that the coNS3/4A plasmidprimed an in vivo functional NS3/4A-specific tumor inhibiting immunitymore rapidly than the wild type plasmid (FIGS. 12A-12C). Two doses ofthe coNS3/4A primed a significantly better NS3/4A-specific tumorinhibiting immunity as compared to the wtNS3/4A plasmid (p<0.05, ANOVA;FIGS. 12A-12C). After three doses the tumor inhibiting immunity was thesame. Thus, the data above verified that the codon optimization of theNS3/4A gene primes NS3-specific CTLs more rapidly.

As set forth herein, the NS3/4A gene can be used as a vaccine. Althoughit had been determined that NS3/4A quickly primed in vivo functionalCTLs, the effect of therapeutic immunization after the injection oftumor cells was analyzed next. Groups of ten C57BL/6 mice werechallenged with 10⁶ NS3/4A-EL-4 tumor cells. One group was immunizedtransdermally with of 4 μg coNS3/4A at six days, and another group at 12days, after tumor challenge. After the therapeutic vaccination bothgroups had significantly smaller tumors as compared to the nonimmunizedcontrol group (p<0.01, respectively, ANOVA; FIG. 13). This confirms thatthe vaccine rapidly primes CTLs, which are able to home to andinfiltrate the NS3/4A-expressing tumors. Thus, gene gun immunizationwith the coNS3/4A plasmid also works as a therapeutic vaccine. That is,gene gun immunization using the coNS3/4A gene six to 12 days afterinoculation of NS3/4A-expressing tumor cells significantly inhibitedtumor growth. Overall, a rapid priming of HCV NS3-specific immuneresponses that are functional in vivo are generated by either DNA basedimmunization with a codon optimized gene or by mRNA amplification by theSFV replicon. By using these approaches, one can prepare very effectivevaccines for the treatment and prevention of chronic HCV infections. Thenext example described in greater detail some of the materials andmethods used in the experiments described herein.

Example 8B Mice

Inbred BALB/c (H-2^(d)) and C57BL/6 (H-2^(b)) mice were obtained fromcommercial vendors (Möllegard, Denmark). B cell (μMT) deficient micewere kindly provided by Dr Karin Sandstedt, Karolinska Institutet,Sweden. CD4 deficient C57BL/6 mice were obtained from the breedingfacility at the Microbiology and Tumorbiology Centre, KarolinskaInstitutet. All mice were female and were used at 4-8 weeks of age atthe start of the experiments.

Recombinant NS3 ATPase/Helicase Domain Protein

The recombinant NS3 (rNS3) protein was kindly provided by Darrell L.Peterson, Department of Biochemistry, Commonwealth University, VA. Theproduction of recombinant NS3 protein (not including NS4A) in E. Colihas been described in the field. Prior to use the rNS3 protein wasdialyzed over night against PBS and sterile filtered.

Generation of a Synthetic Codon Optimized (co) NS3/4A Gene

The sequence of the previously isolated and sequenced unique wtNS3/4Agene was analyzed for codon usage with respect to the most commonly usedcodons in human cells. A total of 435 nucleotides were replaced tooptimize codon usage for human cells. The sequence was sent to RetrogenInc (San Diego, Calif.) for generation of a full-length syntheticcoNS3/4A gene. The coNS3/4A gene had a sequence homology of 79% with theregion at nucleotide positions 3417-5475 of the HCV-1 reference strain.A total of 433 nucleotides differed. On an amino acid level the homologywith the HCV-1 strain was 98% (15 amino acids differed).

The full-length codon optimized 2.1 kb DNA fragment of the HCV genotype1b corresponding to the amino acids 1007 to 1711 encompassing the NS3and NS4A. NS3/NS4A gene fragment was inserted into a Bam HI and Xba Idigested pVAX vector (Invitrogen, San Diego) to give the coNS3/4A-pVAXplasmid. The expression construct was sequenced to ensure correctsequence and reading frame. The protein expression was analysed by an invitro transcription and translation assay. Plasmids were grown incompetent TOP10 E. Coli. (Invitrogen). Plasmid DNA used for in vivoinjection, was purified by using Qiagen DNA purification columnsaccording to the manufacturers instructions (Qiagen GmbH, Hilden, FRG).The concentration of the resulting plasmid DNA was determinedspectrophotometrically (Dynaquant, Pharmacia Biotech, Uppsala, Sweden).Purified DNA was dissolved in sterile phosphate buffer saline (PBS) atconcentrations of 1 mg/ml.

In Vitro Translation Assay

To ensure that the wtNS3/4A and coNS3/4A genes were intact and could betranslated, an in vitro transcription assay is using the prokaryotic T7coupled reticulocyte lysate system (TNT; Promega, Madison, Wis.) wasperformed. To compare the translation efficiency from the two plasmidsthe amount input DNA was diluted in serial dilutions (6 ng to 1 ng)prior to addition to the TNT assay.

Transient Transfections

HepG2 cells were transiently transfected by standard protocols. Inbrief, HepG2 cells were plated into 2.5 cm² wells (0.5×10⁶) in DMEMmedium the day before transfection. Two μg of each plasmid DNA construct(wtNS3/4A and coNS3/4A) was transfected into HepG2 cells using Fugene 6Transfection Reagent (Roche). After transfection, the HepG2 cells wereincubated for 24-48 hrs.

Protein Sample Preparation and Analysis

Cell lysates were analysed by immunoprecipitation followed by SDS-PAGE.In brief, transient transfected HepG2 cells were lysed in RIPA buffer(0.15M NaCl, 50 mM Tris, 1% Triton-X 100, 1% Na-deoxycholate and 1%SDS). The cell lysates were immunoprecipitated with protein A sepharoseand anti-NS3 polyclonal antibody overnight at 4° C. The washed pelletswere re-suspended in SDS sample buffer, heated at 100° C. for 5 minutesprior to SDS-PAGE analysis on 4-12% Bis-Tris gel (Invitrogen) andelectrotransferred onto Nitrocellulose membranes.

Analysis of NS3 Protein Expression

Detection of NS3 protein was done according to manufacturer's protocolby using a chemiluminescence-linked Western blot kit (WesternBreeze;Invitrogen). NS3 protein expression was detected and quantified as achemiluminescent signal by using an NS3-specific polyclonal antibody.Chemiluminescent signals were detected by using the GeneGnome (Syngene,Cambridge, UK). Quantification of chemiluminescence Western blots wasperformed on GeneGnome and units of intensity from each protein band wascalculated and compared to a standard curve of rNS3.

Semliki Forest Virus (SFV) Vectors

Baby Hamster Kidney (BHK)-21 cells were maintained in complete BHKmedium supplemented with 5% FCS, 10% tryptose phosphate broth, 2 mMglutamine, 20 mM Hepes and antibiotics (streptomycin 10 μg/ml andpenicillin 100 IU/ml).

The wtNS3/4A gene was isolated by PCR as Spe1-BStB1 fragment andinserted into the Spe1-BstB1 site of pSFV10Enh containing a 34 aminoacid long translational enhancer sequence of capsid followed by the FMDV2a cleavage peptide. Packaging of recombinant RNA into rSFV particleswas done using a two-helper RNA system. Indirect immunofluorescence ofinfected BHK cells was performed to determine the titre of therecombinant virus stocks.

Immuno Fluorescence

BHK cells were transient transfected with coNS3/4A-pVAX1 according tostandard techniques using Lipofectamine plus reagent (Invitrogen) orinfected by rSFV. NS3 protein was detected by indirectimmunofluorescence.

Immunization Protocols

Groups (5-10 mice/group) of female BALB/c (H-2^(d)) or C57BL/6 (H-2^(b))mice, 4-8 weeks old, were immunized by needle injections of 100 μg ofplasmid DNA encoding individual or multiple HCV proteins. Plasmid DNA inPBS was given intramuscularly (i.m.) in the tibialis anterior (TA)muscle. Where indicated in the text, the mice were injected i.m. with 50μL/TA of 0.01 mM cardiotoxin (Latoxan, Rosans, France) in 0.9% sterilesaline NaCl, five days prior to DNA immunization. The mice were boostedat four-week intervals.

For gene gun based immunizations, plasmid DNA was linked to goldparticles (1 μm) according to protocols supplied by the manufacturer(Bio-Rad Laboratories, Hercules, Calif.). Prior to immunization theabdominal injection area was shaved and the immunization was performedaccording to the manufacturer's protocol at a helium discharge pressureof 500 psi. Each injection dose contained 4 μg of plasmid DNA. The micewere boosted with the same dose at monthly intervals.

For rSFV particle immunizations, mice were immunized subcutaneously, inthe base of the tail, with 1×10⁷ virus particles diluted in PBS(wtNS3/4A-SFV), in a final volume of 100 Peptide immunization wasperformed by subcutaneous immunization in the base of the tail with 100μg peptide mixed 1:1 in complete Freunds adjuvant.

ELISA for Detection of Murine Anti-HCV NS3 Antibodies

Serum for antibody detection and isotyping was collected every second orfourth week after the first immunization by retroorbital bleeding ofisofluorane-anesthetized mice. The enzyme immuno assays were performedas previously described.

Cell Lines

The SP2/0-Ag14 myeloma cell line (H-2^(d)) was maintained in DMEM mediumsupplemented with 10% fetal calf serum (FCS; Sigma Chemicals, St. Louis,Mo.), 2 mM L-Glutamine, 10 mM HEPES, 100 U/ml Penicillin and 100 μg/mlStreptomycin, 1 mM non-essential amino acids, 50 μM β-mercaptoethanol, 1mM sodium pyruvate (GIBCO-BRL, Gaithesburgh, Md.). SP2/0-Ag14 cells withstable expression of NS3/4A were maintained in 800 μg geneticin(G418)/ml complete DMEM medium.

The EL-4 lymphoma (H-2^(b)) cells were maintained in RPMI 1640 mediumsupplemented with 10% FCS, 10 mM HEPES, 1 mM sodium pyruvate, 1 mMnon-essential amino acids, 50 μM β-mercaptoethanol, 100 U/ml Penicillinand 100 μg/ml Streptomycin (GIBCO-BRL). EL-4 cells with stableexpression of NS3/4A were generated by transfection of EL-4 cells withthe linearized NS3/4A-pcDNA3.1 plasmid using the SuperFect (Qiagen GmbH,Hilden, FRG) transfection reagent. The transfection procedure wasperformed according to manufacturer's protocol. Transfected cells werecloned by limiting dilution and selected by addition of 800 μg geneticin(G418)/ml complete RPMI 1640 medium.

RMA-S cells (a kind gift from Professor Klas Kärre, KarolinskaInstitutet, Sweden) were maintained in RPMI 1640 medium supplementedwith 5% FCS, 2 mM L-Glutamine, 100 U/ml Penicillin and 100 μg/mlStreptomycin. All cells were grown in a humidified 37° C., 5% CO₂incubator.

In Vivo Depletion of T Cells

CD4 and CD8 T cell subpopulations were depleted in vivo byintraperitoneal injection of purified hybridoma supernatant. A total of0.4 mg per mouse per injection of anti-CD4 (clone GK1.5) or anti-CD8(clone 53-6.7) was injected on days −3, −2, and −1 before tumorchallenge, and on days 3, 6, 10, and 13 after challenge. Flow cytometricanalysis of peripheral blood mononuclear cell populations at days 0, 3,6, 10, and 13 demonstrated that more than 85% of the CD4 and CD8 T cellswere depleted.

In Vivo Challenge with the NS3/4A-Expressing Tumor Cells

In vivo challenge of immunized mice with the NS3/4A-expressing SP2/0myeloma or EL-4 lymphoma cell line was performed according to the methoddescribed by Encke et al., supra. In brief, groups of BALB/c or C57BL/6mice were immunized with different immunogens at weeks zero, four, andeight as described. Two weeks after the last immunisation 1×10⁶NS3/4A-expressing SP2/0 or EL-4 cells were injected subcutaneously inthe right flank. The kinetics of the tumor growth was determined bymeasuring the tumor size through the skin at days six to 20. Kinetictumor development in two groups of mice was compared using the areaunder the curve (AUC). The mean tumor sizes were compared using theanalysis of variance (ANOVA) test. At day 20 all mice were sacrificed.

To test the therapeutic effect of the vaccines groups of mice wereinoculated with the tumor cells as described above. After six or 12 daysthe mice were immunized once. The tumor growth was monitored from day 6to day 20.

Antibodies and MHC:Ig Fusion Protein

All monoclonal antibodies and MHC:Ig fusion proteins were purchased fromBDB Pharmingen (San Diego, Calif.); Anti-CD16/CD32 (Fc-Block™, clone2.4G2), FITC conjugated anti-CD8 (clone 53-6.7), Cy-Chrome conjugatedanti-CD4 (clone RM4-5), FITC conjugated anti-H-2D^(b) (clone KH95),recombinant soluble dimeric mouse H-2D^(b):Ig, PE conjugated Rat-α MouseIgG1 (clone X56).

Detection of NS3/4A-Specific CTL Activity

Spleen cells from DNA or rSFV immunized C57BL/6 mice were resuspended incomplete RPMI 1640 medium supplemented with 10% FCS, 2 mM L-Glutamine,10 mM HEPES, 100 U/ml Penicillin and 100 μg/ml Streptomycin, 1 mMnon-essential amino acids, 50 μM β-mercaptoethanol, 1 mM sodiumpyruvate. In vitro stimulation was carried out for five days in 25-mlflasks at a final volume of 12 ml, containing 5 U/ml recombinant murineIL-2 (mIL-2; R&D Systems, Minneapolis, Minn., USA). The restimulationculture contained a total of 25×10⁶ immune spleen cells and 2.5×10⁶irradiated (10,000 rad) syngenic EL-4 cells expressing the NS3/4Aprotein. After five days in vitro stimulation a standard ⁵¹Cr-releaseassay was performed. Effector cells were harvested and a four-hour ⁵¹Crassay was performed in 96-well U-bottom plates in a total volume of 200μl. A total of 1×10⁶ target cells (NS3/4A expressing EL-4 cells) waslabelled for one hour at +37° C. with 20 μl of ⁵¹Cr (5 mCi/ml) and thenwashed three times in PBS. Different numbers of effectors and⁵¹Cr-labeled target cells (5×10³ cells/well) were added to wells ateffector:target (E:T) ratios of 60:1, 20:1, and 7:1. The level ofcytolytic activity was determined after incubation of effectors andtargets for 4 hour at +37° C. 100 μl supernatant was harvested and theradioactivity was measured with a γ-counter.

Splenocytes from DNA or rSFV immunised mice were harvested from C57BL/6mice and were resuspended in complete RPMI 1640 medium as previouslydescribed. In brief, in vitro stimulation was carried out for five daysby mixing 25×10⁶ spleen cells and 25×10⁶ irradiated (2,000 rad)syngeneic splenocytes. The restimulation was performed in the presenceof 0.05 μM NS3/4A H-2D^(b) binding peptide (sequence GAVQNEVTL (Seq. Id.No. 37)). After restimulation, a four hour ⁵¹Cr-release assay wasperformed using ⁵¹Cr-labelled peptide pulsed RMA-S cells as targets.Cytotoxic activity was determined at the E:T ratios 60:1, 20:1, and 7:1.

Results were expressed according to the formula: percent specificlysis=(experimental release−spontaneous release)/(maximumrelease−spontaneous release). Experimental release is the meancounts/minute released by the target cells in presence of effectorcells. Maximum release is the radioactivity released after lysis oftarget cells with 10% Triton X-100. Spontaneous release is the leakageof radioactivity into the medium of target cells.

In vitro T-cell depletion experiments were conducted by incubatingeffector cells with either an anti-CD4, or anti-CD8, monoclonal antibodycontaining hybridoma supernatant (clone RL 172.4; anti-CD4, or clone31M; anti-CD8) for 30 minutes at 4° C. The cells were then washed andincubated at 37° C. for 1 hr with complement (1/20 dilution of lowtoxicity rabbit complement; Saxon, UK) before performing the CTL assaydescribed above.

Quantification of NS3/4A-Specific CTLs by Flow Cytometry

The frequency of NS3-peptide specific CD8+ T cells were analysed byex-vivo staining of spleen cells from DNA or rSFV immunized mice withrecombinant soluble dimeric mouse H-2D^(b):Ig fusion protein aspreviously described. In brief, spleen cells were resuspended in PBS/1%FCS (FACS buffer) and incubated with Fc-blocking antibodies. Cells werethen washed and incubated with H-2D^(b):Ig preloaded with NS3/4A derivedpeptide. Afterwards, cells were washed and incubated with PE conjugatedRat-α Mouse IgG1 antibody, FITC conjugated α-mouse CD8 antibody andCy-Chrome α-mouse CD4 antibody. After washing, the cells were diluted inFACS buffer containing Propidium Iodide (PI). Approximately 200,000total events from each sample were acquired on a FACSCalibur (BDB) anddead cells (PI positive cells) were excluded in the analysis.

Statistical Analysis

Fisher's exact test was used for frequency analysis and Mann-WhitneyU-test was used for comparing values from two groups. Kinetic tumordevelopment in two groups of mice was compared using the area under thecurve (AUC). AUC values were compared using analysis of variance(ANOVA). The calculations were performed using the Macintosh version ofthe StatView software (version 5.0).

The compositions described herein may contain other ingredients orcompounds in addition to nucleic acids and/or polypeptides, including,but not limited to, various other peptides, adjuvants, binding agents,excipients such as stabilizers (to promote long term storage),emulsifiers, thickening agents, salts, preservatives, solvents,dispersion media, coatings, antibacterial and antifungal agents,isotonic and absorption delaying agents and the like. See e.g., U.S.application Ser. No. 09/929,955 and U.S. application Ser. No.09/930,591. These compositions are suitable for treatment of animals,particularly mammals, either as a preventive measure to avoid a diseaseor condition or as a therapeutic to treat animals already afflicted witha disease or condition.

Many other ingredients may also be present in the compositions providedherein. For example, the adjuvant and antigen can be employed inadmixture with conventional excipients (e.g., pharmaceuticallyacceptable organic or inorganic carrier substances suitable forparenteral, enteral (e.g., oral) or topical application that do notdeleteriously react with the adjuvant (e.g., ribavirin) and/or antigen).Suitable pharmaceutically acceptable carriers include, but are notlimited to, water, salt solutions, alcohols, gum arabic, vegetable oils,benzyl alcohols, polyethylene glycols, gelatine, carbohydrates such aslactose, amylose or starch, magnesium stearate, talc, silicic acid,viscous paraffin, perfume oil, fatty acid monoglycerides anddiglycerides, pentaerythritol fatty acid esters, hydroxymethylcellulose, polyvinyl pyrrolidone, etc. Many more suitable carriersare described in Remington's Pharmaceutical Sciences, 15th Edition,Easton:Mack Publishing Company, pages 1405-1412 and 1461-1487 (1975) andThe National Formulary XIV, 14th Edition, Washington, AmericanPharmaceutical Association (1975).

The gene constructs described herein, in particular, can be formulatedwith or administered in conjunction with agents that increase uptakeand/or expression of the gene construct by the cells relative to uptakeand/or expression of the gene construct by the cells that occurs whenthe identical genetic vaccine is administered in the absence of suchagents. Such agents and the protocols for administering them inconjunction with gene constructs are described in PCT Patent ApplicationSerial Number PCT/US94/00899 filed Jan. 26, 1994. Examples of suchagents include: CaPO₄, DEAE dextran, anionic lipids; extracellularmatrix-active enzymes; saponins; lectins; estrogenic compounds andsteroidal hormones; hydroxylated lower alkyls; dimethyl sulfoxide(DMSO); urea; and benzoic acid esters anilides, amidines, urethanes andthe hydrochloride salts thereof, such as those of the family of localanesthetics. In addition, the gene constructs can be encapsulatedwithin/administered in conjunction with lipids/polycationic complexes.

Vaccines and immunogenic compositions can be sterilized and if desiredmixed with auxiliary agents, e.g., lubricants, preservatives,stabilizers, wetting agents, emulsifiers, salts for influencing osmoticpressure, buffers, coloring, flavoring and/or aromatic substances andthe like that do not deleteriously react with the adjuvant or theadministered nucleic acid or peptide.

The effective dose and method of administration of a particularformulation can vary based on the individual patient and the type andstage of the disease, as well as other factors known to those of skillin the art. Therapeutic efficacy and toxicity can be determined bystandard pharmaceutical procedures in cell cultures or experimentalanimals, e.g., ED50 (the dose therapeutically effective in 50% of thepopulation). The data obtained from cell culture assays and animalstudies can be used to formulate a range of dosage for human use. Thedosage lies preferably within a range of circulating concentrations thatinclude the ED50 with no toxicity. The dosage varies within this rangedepending upon the type of adjuvant derivative and antigen, the dosageform employed, the sensitivity of the patient, and the route ofadministration.

Since many adjuvants (e.g., ribavirin) have been on the market forseveral years, many dosage forms and routes of administration are known.All known dosage forms and routes of administration can be providedwithin the context of the embodiments described herein. Preferably, anamount of adjuvant that is effective to enhance an immune response to anantigen in an animal can be considered to be an amount that issufficient to achieve a blood serum level of antigen approximately0.25-12.5 μg/ml in the animal, preferably, about 2.5 μg/ml. In someembodiments, the amount of adjuvant is determined according to the bodyweight of the animal to be given the vaccine. Accordingly, the amount ofadjuvant in a vaccine formulation can be from about 0.1-6.0 mg/kg bodyweight. That is, some embodiments have an amount of adjuvant thatcorresponds to approximately 0.1-1.0 mg/kg, 1.1-2.0 mg/kg, 2.1-3.0mg/kg, 3.1-4.0 mg/kg, 4.1-5.0 mg/kg, and 5.1-6.0 mg/kg body weight of ananimal. More conventionally, the vaccines contain approximately 0.25mg-2000 mg of adjuvant. That is, some embodiments have approximately 250μg, 500 μg, 1 mg, 25 mg, 50 mg, 100 mg, 150 mg, 200 mg, 250 mg, 300 mg,350 mg, 400 mg, 450 mg, 500 mg, 550 mg, 600 mg, 650 mg, 700 mg, 750 mg,800 mg, 850 mg, 900 mg, 1 g, 1.1 g, 1.2 g, 1.3 g, 1.4 g, 1.5 g, 1.6 g,1.7 g, 1.8 g, 1.9 g, and 2 g of adjuvant.

As one of skill in the art will appreciate, the amount of antigens in avaccine can vary depending on the type of antigen and itsimmunogenicity. The amount of antigens in the vaccine can varyaccordingly. Nevertheless, as a general guide, the vaccines can haveapproximately 1 μg, 5 μg, 1 μg, 20 μg, 40 μg, 80 μg, 100 μg, 0.25 mg-5mg, 5-10 mg, 10-100 mg, 100-500 mg, and upwards of 2000 mg of an antigendescribed herein, for example. Preferably, the amount of antigen is 0.1μg-1 mg, desirably, 0.1 μg-100 μg, preferably 3 μg-50 μg, and, mostpreferably, 7 μg, 8 μg, 9 μg, 10 μg, 11 μg-20 μg, when said antigen is anucleic acid.

In some approaches described herein, the exact amount of adjuvant and/orantigen is chosen by the individual physician in view of the patient tobe treated. Further, the amounts of adjuvant can be added in combinationto or separately from the same or equivalent amount of antigen and theseamounts can be adjusted during a particular vaccination protocol so asto provide sufficient levels in light of patient-specific orantigen-specific considerations. In this vein, patient-specific andantigen-specific factors that can be taken into account include, but arenot limited to, the severity of the disease state of the patient, age,and weight of the patient, diet, time and frequency of administration,drug combination(s), reaction sensitivities, and tolerance/response totherapy.

Ribavirin

Nucleoside analogs have been widely used in anti-viral therapies due totheir capacity to reduce viral replication. (Hosoya et al., J. Inf.Dis., 168:641-646 (1993)). ribavirin(1-β-D-ribofuranosyl-1,2,4-triazole-3-carboxamide) is a syntheticguanosine analog that has been used to inhibit RNA and DNA virusreplication. (Huffman et al., Antimicrob. Agents. Chemother., 3:235(1973); Sidwell et al., Science, 177:705 (1972)). Ribavirin has beenshown to be a competitive inhibitor of inositol mono-phosphate (IMP)dehydrogenase (IMPDH), which converts IMP to IMX (which is thenconverted to GMP). De Clercq, Anti viral Agents: characteristic activityspectrum depending on the molecular target with which they interact,Academic press, Inc., New York N.Y., pp. 1-55 (1993). Intracellularpools of GTP become depleted as a result of long term ribavirintreatment.

In addition to antiviral activity, investigators have observed that someguanosine analogs have an effect on the immune system. (U.S. Pat. Nos.6,063,772 and 4,950,647). Ribavirin has been shown to inhibit functionalhumoral immune responses (Peavy et al., J. Immunol., 126:861-864 (1981);Powers et al., Antimicrob. Agents. Chemother., 22:108-114 (1982)) andIgE-mediated modulation of mast cell secretion. (Marquardt et al., J.Pharmacol. Exp. Therapeutics, 240:145-149 (1987)). Some investigatorsreport that a daily oral therapy of ribavirin has an immune modulatingeffect on humans and mice. (Hultgren et al., J. Gen. Virol.,79:2381-2391 (1998) and Cramp et al., Gastron. Enterol., 118:346-355(2000)). Nevertheless, the current understanding of the effects ofribavirin on the immune system is in its infancy. As disclosed below,ribavirin was found to be a potent adjuvant.

Example 9

In a first set of experiments, groups of three to five Balb/c mice (BKUniversal, Uppsala, Sweden) were immunized i.p or s.c. (e.g., at thebase of the tail) with 10 μg or 100 μg of recombinant hepatitis C virusnon-structural 3 (rNS3) protein. The rNS3 was dissolved in phosphatebuffered saline (PBS) alone or PBS containing 1 mg ribavirin (obtainedfrom ICN, Costa Mesa, Calif.). Mice were injected with a total volume of1000 per injection.

At two and four weeks following i.p. immunization, all mice were bled byretro-orbital sampling. Serum samples were collected and analyzed forthe presence of antibodies to rNS3. To determine the antibody titer, anenzyme immunoassay (EIA) was performed. (See e.g., Hultgren et al., JGen Virol. 79:2381-91 (1998) and Hultgren et al., Clin. Diagn. Lab.Immunol. 4:630-632 (1997)). The antibody levels were recorded as thehighest serum dilution giving an optical density at 405 nm more thantwice that of non-immunized mice.

Mice that received 10 μg or 100 μg rNS3 mixed with 1 mg ribavirin in PBSdisplayed consistently higher levels of NS3 antibodies. The antibodytiter that was detected by EIA at two weeks post-immunization is shownin FIG. 14. The vaccine formulations having 1 mg of ribavirin and either10 μg or 100 μg of rNS3 induced a significantly greater antibody titerthan the vaccine formulations composed of only rNS3.

In a second set of experiments, groups of eight Balb/c mice wereimmunized intraperitoneally with 10 or 50 μg of rNS3 in 100 μl phosphatebuffered saline containing either 0 mg, 1 mg, 3 mg, or 10 mg ribavirin(Sigma). At four, six and eight weeks the mice were bled and serum wasseparated and frozen. After completion of the study, sera were testedfor the levels of antibodies to recombinant NS3, as described above.Mean antibody levels to rNS3 were compared between the groups usingStudent's t-test (parametric analysis) or Mann-Whitney (non-parametricanalysis) and the software package StatView 4.5 (Abacus Concepts,Berkeley, Calif.). The adjuvant effect of ribavirin when added in threedoses to 10 μg of rNS3 are provided in TABLE 14. The adjuvant effect ofribavirin when added in three doses to 50 μg of rNS3 are provided inTABLE 15. Parametrical comparison of the mean rNS3 antibody titres inmice receiving different 10 μg or 50 μg of rNS3 and different doses ofribavirin are provided in TABLES 15 and 16, respectively.Non-parametrical comparison of mean NS3 antibody titres in micereceiving different 10 μg or 50 μg of rNS3 and different doses ofribavirin are provided in TABLES 17-19, respectively. The values givenrepresent end point titres to recombinant rNS3.

TABLE 14 Amount Amount ribavirin immunogen Mouse Antibody titre to rNS3at indicated week (mg/dose) (μg/dose) ID Week 4 Week 6 Week 8 None 105:1 300 1500 1500 None 10 5:2 <60 7500 1500 None 10 5:3 <60 1500 300None 10 5:4 60 1500 1500 None 10 5:5 <60 1500 nt None 10 5:6 60 15001500 None 10 5:7 <60 7500 7500 None 10 5:8 300 37500 7500 Group meantitre (mean ± SD) 180 ± 139  7500 ± 12421 3042 ± 3076 1 10 6:1 300 3750037500 1 10 6:2 <60 1500 1500 1 10 6:3 300 37500 187500 1 10 6:4 30037500 7500 1 10 6:5 60 nt nt 1 10 6:6 <60 37500 7500 1 10 6:7 <60 375007500 1 10 6:8 300 7500 7500 Group mean titre (mean ± SD) 252 ± 107 28071± 16195 36642 ± 67565 3 10 7:1 60 37500 7500 3 10 7:2 60 37500 37500 310 7:3 300 7500 7500 3 10 7:4 300 37500 7500 3 10 7:5 300 37500 37500 310 7:6 300 37500 37500 3 10 7:7 60 7500 7500 3 10 7:8 60 37500 37500Group mean titre (mean ± SD) 180 ± 128 30000 ± 13887 22500 ± 34637 10 108:1 300 37500 37500 10 10 8:2 300 37500 37500 10 10 8:3 <60 300 300 1010 8:4 60 7500 7500 10 10 8:5 <60 300 300 10 10 8:6 <60 37500 37500 1010 8:7 <60 7500 7500 10 10 8:8 <60 nt nt Group mean titre (mean ± SD)220 ± 139 18300 ± 18199 18300 ± 18199

TABLE 15 Amount Amount Antibody titre to rNS3 at indicated ribavirinimmunogen Mouse week (mg/dose) (μg/dose) ID Week 4 Week 6 Week 8 None 501:1 60 7500 7500 None 50 1:2 60 7500 7500 None 50 1:3 60 7500 7500 None50 1:4 <60 1500 300 None 50 1:5 300 37500 37500 None 50 1:6 60 7500 7500None 50 1:7 60 37500 7500 None 50 1:8 — — — Group mean titre (mean ± SD)100 ± 98  15214 ± 15380 10757 ± 12094 1 50 2:1 60 7500 7500 1 50 2:2 30037500 7500 1 50 2:3 60 187500 7500 1 50 2:4 60 37500 187500 1 50 2:5 6037500 7500 1 50 2:6 60 37500 37500 1 50 2:7 300 37500 7500 1 50 2:8 30037500 37500 Group mean titre (mean ± SD) 150 ± 124 52500 ± 55549 37500 ±62105 3 50 3:1 60 37500 7500 3 50 3:2 300 37500 37500 3 50 3:3 300 375007500 3 50 3:4 60 37500 7500 3 50 3:5 300 37500 7500 3 50 3:6 60 375007500 3 50 3:7 — 7500 37500 3 50 3:8 1500 7500 37500 Group mean titre(mean ± SD) 387 ± 513 30000 ± 13887 18750 ± 15526 10 50 4:1 300 75007500 10 50 4:2 300 37500 37500 10 50 4:3 60 7500 7500 10 50 4:4 60 75007500 10 50 4:5 60 1500 1500 10 50 4:6 60 7500 37500 10 50 4:7 — 75007500 10 50 8:8 60 37500 7500 Group mean titre (mean ± SD) 140 ± 12410929 ± 11928 15214 ± 15380

TABLE 16 Group Week Mean ± SD Group Mean ± SD analysis p-value 10 μgNS3/ 4 180 ± 139 10 μg NS3/ 252 ± 107 Students 0.4071 no ribavirin 1 mgribavirin t-test 6  7500 ± 12421 28071 ± 16195 Students 0.0156* t-test 83042 ± 3076 36642 ± 67565 Students 0.2133 t-test 10 μg NS3/ 4 180 ± 13910 μg NS3/ 180 ± 128 Students 1.000 no ribavirin 3 mg ribavirin t-test 6 7500 ± 12421 30000 ± 13887 Students 0.0042** t-test 8 3042 ± 3076 22500± 34637 Students 0.0077** t-test 10 μg NS3/ 4 180 ± 139 10 μg NS3/ 220 ±139 Students 0.7210 no ribavirin 10 mg ribavirin t-test 6  7500 ± 1242118300 ± 18199 Students 0.1974 t-test 8 3042 ± 3076 18300 ± 18199Students 0.0493* t-test

TABLE 17 Group Week Mean ± SD Group Mean ± SD analysis p-value 50 μgNS3/ 4 100 ± 98  50 μg NS3/ 150 ± 124 Students 0.4326 no ribavirin 1 mgribavirin t-test 6 15214 ± 15380 52500 ± 55549 Students 0.1106 t-test 810757 ± 12094 37500 ± 62105 Students 0.2847 t-test 50 μg NS3/ 4 100 ±98  50 μg NS3/ 387 ± 513 Students 0.2355 no ribavirin 3 mg ribavirint-test 6 15214 ± 15380 30000 ± 13887 Students 0.0721 t-test 8 10757 ±12094 18750 ± 15526 Students 0.2915 t-test 50 μg NS3/ 4 100 ± 98  50 μgNS3/ 140 ± 124 Students 0.5490 no ribavirin 10 mg ribavirin t-test 615214 ± 15380 10929 ± 11928 Students 0.5710 t-test 8 10757 ± 12094 15214± 15380 Students 0.5579 t-test Significance levels: NS = notsignificant; * = p < 0.05; ** = p < 0.01; *** = p < 0.001

TABLE 18 Group Week Mean ± SD Group Mean ± SD analysis p-value 10 μgNS3/ 4 180 ± 139 10 μg NS3/ 252 ± 107 Mann- 0.4280 no ribavirin 1 mgribavirin Whitney 6  7500 ± 12421 28071 ± 16195 Mann- 0.0253* Whitney 83042 ± 3076 36642 ± 67565 Mann- 0.0245* Whitney 10 μg NS3/ 4 180 ± 13910 μg NS3/ 180 ± 128 Mann- 0.0736 no ribavirin 3 mg ribavirin Whitney 6 7500 ± 12421 30000 ± 13887 Mann- 0.0050** Whitney 8 3042 ± 3076 22500 ±34637 Mann- 0.0034** Whitney 10 μg NS3/ 4 180 ± 139 10 μg NS3/ 220 ± 139Mann- 0.8986 no ribavirin 10 mg ribavirin Whitney 6  7500 ± 12421 18300± 18199 Mann- 0.4346 Whitney 8 3042 ± 3076 18300 ± 18199 Mann- 0.2102Whitney

TABLE 19 Group Week Mean ± SD Group Mean ± SD analysis p-value 50 μgNS3/ 4 100 ± 98  50 μg NS3/ 150 ± 124 Mann- 0.1128 no ribavirin 1 mgribavirin Whitney 6 15214 ± 15380 52500 ± 55549 Mann- 0.0210* Whitney 810757 ± 12094 37500 ± 62105 Mann- 0.1883 Whitney 50 μg NS3/ 4 100 ± 98 50 μg NS3/ 387 ± 513 Mann- 0.1400 no ribavirin 3 mg ribavirin Whitney 615214 ± 15380 30000 ± 13887 Mann- 0.0679 Whitney 8 10757 ± 12094 18750 ±15526 Mann- 0.2091 Whitney 50 μg NS3/ 4 100 ± 98  50 μg NS3/ 140 ± 124Mann- 0.4292 no ribavirin 10 mg ribavirin Whitney 6 15214 ± 15380 10929± 11928 Mann- 0.9473 Whitney 8 10757 ± 12094 15214 ± 15380 Mann- 0.6279Whitney Significance levels: NS = not significant; *= p < 0.05; **= p <0.01; ***= p < 0.001The data above demonstrates that ribavirin facilitates or enhances animmune response to an HCV antigen or HCV epitopes. A potent immuneresponse to rNS3 was elicited after immunization with a vaccinecomposition comprising as little as 1 mg ribavirin and 10 μg of rNS3antigen. The data above also provide evidence that the amount ofribavirin that is sufficient to facilitate an immune response to anantigen is between 1 and 3 mg per injection for a 25-30 g Balb/c mouse.It should be realized, however, that these amounts are intended forguidance only and should not be interpreted to limit the scope of theinvention in any way. Nevertheless, the data shows that vaccinecompositions comprising approximately 1 to 3 mg doses of ribavirininduce an immune response that is more than 12 times higher than theimmune response elicited in the absence of without ribavirin. Thus,ribavirin has a significant adjuvant effect on the humoral immuneresponse of an animal and thereby, enhances or facilitates the immuneresponse to the antigen. The example below describes experiments thatwere performed to better understand the amount of ribavirin needed toenhance or facilitate an immune response to an antigen.

Example 10

To determine a dose of ribavirin that is sufficient to provide anadjuvant effect, the following experiments were performed. In a firstset of experiments, groups of mice (three per group) were immunized witha 20 μg rNS3 alone or a mixture of 20 μg rNS3 and 0.1 mg, 1 mg, or 10 mgribavirin. The levels of antibody to the antigen were then determined byEIA. The mean endpoint titers at weeks 1 and 3 were plotted and areshown in FIG. 15. It was discovered that the adjuvant effect provided byribavirin had different kinetics depending on the dose of ribavirinprovided. For example, even low doses (<1 mg) of ribavirin were found toenhance antibody levels at week one but not at week three, whereas,higher doses (1-10 mg) were found to enhance antibody levels at weekthree.

A second set of experiments was also performed. In these experiments,groups of mice were injected with vaccine compositions comprisingvarious amounts of ribavirin and rNS3 and the IgG response in theseanimals was monitored. The vaccine compositions comprised approximately100 μl phosphate buffered saline and 20 μg rNS3 with or without 0.1 mg,1.0 mg, or 10 mg ribavirin (Sigma). The mice were bled at week six andrNS3-specific IgG levels were determined by EIA as described previously.As shown in TABLE 20, the adjuvant effects on the sustained antibodylevels were most obvious in the dose range of 1 to 10 mg per injectionfor a 25-30 g mouse.

TABLE 20 Amount (mg) ribavirin Endpoint titre of rNS3 mixed with theMouse IgG at indicated week Immunogen immunogen ID Week 1 Week 2 Week 320 μg rNS3 None 1 60 360 360 20 μg rNS3 None 2 360 360 2160 20 μg rNS3None 3 360 2160 2160 Mean 260 ± 173  960 ± 1039 1560 ± 1039 20 μg rNS30.1 4 2160 12960 2160 20 μg rNS3 0.1 5 60 60 60 20 μg rNS3 0.1 6 <602160 2160 1110 ± 1484 5060 ± 6921 1460 ± 1212 20 μg rNS3 1.0 7 <60 6012960 20 μg rNS3 1.0 8 <60 2160 2160 20 μg rNS3 1.0 9 360 2160 2160 Mean360 1460 ± 1212 5760 ± 6235 20 μg rNS3 10.0 10 360 12960 77760 20 μgrNS3 10.0 11 <60 2160 12960 20 μg rNS3 10.0 12 360 2160 2160 Mean 3605760 ± 6235 30960 ± 40888

In a third set of experiments, the adjuvant effect of ribavirin afterprimary and booster injections was investigated. In these experiments,mice were given two intraperitoneal injections of a vaccine compositioncomprising 10 μg rNS3 with or without ribavirin and the IgG subclassresponses to the antigen was monitored, as before. Accordingly, micewere immunized with 100 μl phosphate buffered containing 10 μgrecombinant NS3 alone, with or without 0.1 or 1.0 mg ribavirin (Sigma)at weeks 0 and 4. The mice were bled at week six and NS3-specific IgGsubclasses were determined by EIA as described previously. As shown inTABLE 21, the addition of ribavirin to the immunogen prior to theinjection does not change the IgG subclass response in the NS3-specificimmune response. Thus, the adjuvant effect of a vaccine compositioncomprising ribavirin and an antigen can not be explained by a shift inof the Th1/Th2-balance. It appears that another mechanism may beresponsible for the adjuvant effect of ribavirin.

TABLE 21 Amount (mg) ribavirin Endpoint titre of indicated mixed withNS3 IgG subclass Immunogen the immunogen Mouse ID IgG1 IgG2a IgG2b IgG310 μg rNS3 None 1 360 60 <60 60 10 μg rNS3 None 2 360 <60 <60 60 10 μgrNS3 None 3 2160 60 <60 360 Mean 960 ± 1039 60 — 160 ± 173 10 μg rNS30.1 4 360 <60 <60 60 10 μg rNS3 0.1 5 60 <60 <60 <60 10 μg rNS3 0.1 62160 60 60 360 860 ± 1136 60 60 210 ± 212 10 μg rNS3 1.0 7 2160 <60 <6060 10 μg rNS3 1.0 8 360 <60 <60 <60 10 μg rNS3 1.0 9 2160 <60 <60 60Mean 1560 ± 1039  — — 60

The data presented in this example further verify that ribavirin can beadministered as an adjuvant and establish that that the dose ofribavirin can modulate the kinetics of the adjuvant effect. The examplebelow describes another assay that was performed to evaluate the abilityof ribavirin to enhance or facilitate an immune response to an antigen.

Example 11

This assay can be used with any ribavirin derivative or combinations ofribavirin derivatives to determine the extent that a particular vaccineformulation modulates a cellular immune response. To determine CD4⁺ Tcell responses to a ribavirin-containing vaccine, groups of mice wereimmunized s.c. with either 100 μg rNS3 in PBS or 100 μg rNS3 and 1 mgribavirin in PBS. The mice were sacrificed ten days post-immunizationand their lymph nodes were harvested and drained. In vitro recall assayswere then performed. (See e.g., Hultgren et al., J Gen Virol. 79:2381-91(1998) and Hultgren et al., Clin. Diagn. Lab. Immunol. 4:630-632(1997)). The amount of CD4⁺ T cell proliferation was determined at 96 hof culture by the incorporation of [³H]thymidine.

As shown in FIG. 16, mice that were immunized with 100 μg rNS3 mixedwith 1 mg ribavirin had a much greater T cell proliferative responsethan mice that were immunized with 100 μg rNS3 in PBS. This dataprovides more evidence that ribavirin enhances or facilitates a cellularimmune response (e.g., by promoting the effective priming of T cells).

Additional experiments were conducted to verify that ribavirin enhancesthe immune response to commercially available vaccine preparations. Theexample below describes the use of ribavirin in conjunction with acommercial HBV vaccine preparation.

Example 12

The adjuvant effect of ribavirin was tested when mixed with two doses ofa commercially available vaccine containing HBsAg and alum. (Engerix,SKB). Approximately 0.2 μg or 2 μg of Engerix vaccine was mixed witheither PBS or 1 mg ribavirin in PBS and the mixtures were injected intraperitoneally into groups of mice (three per group). A booster containingthe same mixture was given on week four and all mice were bled on weeksix. The serum samples were diluted from 1:60 to 1:37500 and thedilutions were tested by EIA, as described above, except that purifiedhuman HBsAg was used as the solid phase antigen. As shown in TABLE 22,vaccine formulations having ribavirin enhanced the response to 2 μg ofan existing vaccine despite the fact that the vaccine already containedalum. That is, by adding ribavirin to a suboptimal vaccine dose (i.e.,one that does not induce detectable antibodies alone) antibodies becamedetectable, providing evidence that the addition of ribavirin allows forthe use of lower antigen amounts in a vaccine formulation withoutcompromising the immune response.

TABLE 22 End point antibody titer to HBsAg in EIA 0.02 μg Engerix 0.2 μgEngerix No ribavirin 1 mg ribavirin No ribavirin 1 mg ribavirin Week #1#2 #3 #1 #2 #3 #1 #2 #3 #1 #2 #3 6 <60 <60 <60 <60 <60 <60 <60 <60 <60300 60 <60

The ribavirin used in the experiments above was obtained from commercialsuppliers (e.g., Sigma and ICN). The ribavirin that can be used with theembodiments described herein can also be obtained from commercialsuppliers or can be synthesized. The ribavirin and/or the antigen can beformulated with and without modification. For example, the ribavirin canbe modified or derivatized to make a more stable molecule and/or a morepotent adjuvant. By one approach, the stability of ribavirin can beenhanced by coupling the molecules to a support such as a hydrophilicpolymer (e.g., polyethylene glycol).

Many more ribavirin derivatives can be generated using conventionaltechniques in rational drug design and combinatorial chemistry. Forexample, Molecular Simulations Inc. (MSI), as well as many othersuppliers, provide software that allows one of skill to build acombinatorial library of organic molecules. The C2.Analog Builderprogram, for example, can be integrated with MSI's suite of Cerius2molecular diversity software to develop a library of ribavirinderivatives that can be used with the embodiments described herein. (Seee.g., http://msi.com/life/products/cerius2/index.html).

By one approach, the chemical structure of ribavirin is recorded on acomputer readable media and is accessed by one or more modeling softwareapplication programs. The C2.Analog Builder program in conjunction withC2Diversity program allows the user to generate a very large virtuallibrary based on the diversity of R-groups for each substituentposition, for example. Compounds having the same structure as themodeled ribavirin derivatives created in the virtual library are thenmade using conventional chemistry or can be obtained from a commercialsource.

The newly manufactured ribavirin derivatives can then be screened inassays, which determine the extent of adjuvant activity of the moleculeand/or the extent of its ability to modulate of an immune response. Someassays may involve virtual drug screening software, such as C2.Ludi.C2.Ludi is a software program that allows a user to explore databases ofmolecules (e.g., ribavirin derivatives) for their ability to interactwith the active site of a protein of interest (e.g., RAC2 or another GTPbinding protein). Based upon predicted interactions discovered with thevirtual drug screening software, the ribavirin derivatives can beprioritized for further characterization in conventional assays thatdetermine adjuvant activity and/or the extent of a molecule to modulatean immune response. The section below provides more explanationconcerning the methods of using the compositions described herein.

Methods of Using the Vaccine Compositions and Immunogen Preparations

Routes of administration of the embodiments described herein include,but are not limited to, transdermal, parenteral, gastrointestinal,transbronchial, and transalveolar. Transdermal administration can beaccomplished by application of a cream, rinse, gel, etc. capable ofallowing the adjuvant and HCV antigen to penetrate the skin. Parenteralroutes of administration include, but are not limited to, electrical ordirect injection such as direct injection into a central venous line,intravenous, intramuscular, intraperitoneal, intradermal, orsubcutaneous injection. Gastrointestinal routes of administrationinclude, but are not limited to, ingestion and rectal. Transbronchialand transalveolar routes of administration include, but are not limitedto, inhalation, either via the mouth or intranasally.

Compositions having the adjuvant and HCV antigen that are suitable fortransdermal administration include, but are not limited to,pharmaceutically acceptable suspensions, oils, creams, and ointmentsapplied directly to the skin or incorporated into a protective carriersuch as a transdermal device (“transdermal patch”). Examples of suitablecreams, ointments, etc. can be found, for instance, in the Physician'sDesk Reference. Examples of suitable transdermal devices are described,for instance, in U.S. Pat. No. 4,818,540 issued Apr. 4, 1989 to Chinen,et al.

Compositions having the adjuvant and HCV antigen that are suitable forparenteral administration include, but are not limited to,pharmaceutically acceptable sterile isotonic solutions. Such solutionsinclude, but are not limited to, saline, phosphate buffered saline andoil preparations for injection into a central venous line, intravenous,intramuscular, intraperitoneal, intradermal, or subcutaneous injection.

Compositions having the adjuvant and HCV antigen that are suitable fortransbronchial and transalveolar administration include, but not limitedto, various types of aerosols for inhalation. Devices suitable fortransbronchial and transalveolar administration of these are alsoembodiments. Such devices include, but are not limited to, atomizers andvaporizers. Many forms of currently available atomizers and vaporizerscan be readily adapted to deliver vaccines having ribavirin and anantigen.

Compositions having the adjuvant and HCV antigen that are suitable forgastrointestinal administration include, but not limited to,pharmaceutically acceptable powders, pills or liquids for ingestion andsuppositories for rectal administration.

The gene constructs described herein, in particular, may be administeredby means including, but not limited to, traditional syringes, needlelessinjection devices, or “microprojectile bombardment gene guns”.Alternatively, the genetic vaccine may be introduced by various meansinto cells that are removed from the individual. Such means include, forexample, ex vivo transfection, electroporation, microinjection andmicroprojectile bombardment. After the gene construct is taken up by thecells, they are reimplanted into the individual. It is contemplated thatotherwise non-immunogenic cells that have gene constructs incorporatedtherein can be implanted into the individual even if the vaccinatedcells were originally taken from another individual.

According to some embodiments, the gene construct is administered to anindividual using a needleless injection device. According to someembodiments, the gene construct is simultaneously administered to anindividual intradermally, subcutaneously and intramuscularly using aneedleless injection device. Needleless injection devices are well knownand widely available. One having ordinary skill in the art can,following the teachings herein, use needleless injection devices todeliver genetic material to cells of an individual. Needleless injectiondevices are well suited to deliver genetic material to all tissue. Theyare particularly useful to deliver genetic material to skin and musclecells. In some embodiments, a needleless injection device may be used topropel a liquid that contains DNA molecules toward the surface of theindividual's skin. The liquid is propelled at a sufficient velocity suchthat upon impact with the skin the liquid penetrates the surface of theskin, permeates the skin and muscle tissue therebeneath. Thus, thegenetic material is simultaneously administered intradermally,subcutaneously and intramuscularly. In some embodiments, a needlelessinjection device may be used to deliver genetic material to tissue ofother organs in order to introduce a nucleic acid molecule to cells ofthat organ.

Preferred embodiments concern methods of treating or preventing HCVinfection. In these embodiments, an animal in need is provided an HCVantigen (e.g., a peptide antigen or nucleic acid-based antigen, asdescribed herein (SEQ. ID. NOs.: 1-27, 35-36, and 40-220 (includingwild-type and codon optimized sequences encoding SEQ ID NOs: 40-220) andan amount of adjuvant sufficient to exhibit an adjuvant activity in saidanimal. Accordingly, an animal can be identified as one in need by usingcurrently available diagnostic testing or clinical evaluation. Theadjuvant and antigen can be provided separately or in combination, andother adjuvants (e.g., oil, alum, or other agents that enhance an immuneresponse) can also be provided to the animal in need.

Other embodiments of the invention include methods of enhancing animmune response to an HCV antigen by providing an animal in need with anamount of adjuvant (e.g., ribavirin) and one or more of SEQ. ID. NOs.:1-11, 35-36, and 40-220 (or a wild type or codon-optimized nucleic acidencoding SEQ ID NOs: 40-220) or a fragment thereof, preferably SEQ. ID.NOs.: 12-27 that is effective to enhance said immune response. In theseembodiments, an animal in need of an enhanced immune response to anantigen is identified by using currently available diagnostic testing orclinical evaluation. By one approach, for example, an uninfectedindividual is provided with the vaccine compositions described above inan amount sufficient to elicit a cellular and humoral immune response toNS3 so as to protect said individual from becoming infected with HCV. Inanother embodiment, an HCV-infected individual is identified andprovided with a vaccine composition comprising ribavirin and NS3 in anamount sufficient to enhance the cellular and humoral immune responseagainst NS3 so as to reduce or eliminate the HCV infection. Suchindividual may be in the chronic or acute phase of the infection. In yetanother embodiment, an HCV-infected individual suffering from HCC isprovided with a composition comprising an adjuvant and the NS3/4A fusiongene in an amount sufficient to elicit a cellular and humoral immuneresponse against NS3-expressing tumor cells.

The next section describes some of the peptide embodiments of theinvention.

HCV Peptides

The embodied HCV peptides or derivatives thereof, include but are notlimited to, those containing as a primary amino acid sequence all of theamino acid sequence substantially as depicted in the Sequence Listing(SEQ. ID. NOs.: 2-11, 36, and SEQ ID NOs: 40-220) and fragments of SEQ.ID. NOs.: 2-11 and SEQ. ID. NO.: 36 that are at least four amino acidsin length (e.g., SEQ. ID. NOs.: 14-16) including altered sequences inwhich functionally equivalent amino acid residues are substituted forresidues within the sequence resulting in a silent change. Preferredfragments of a sequence of SEQ. ID. NOs.: 2-11 and SEQ. ID. NO.: 36 areat least four amino acids and comprise amino acid sequence unique to thediscovered NS3/4A peptide or mutants thereof including altered sequencesin which functionally equivalent amino acid residues are substituted forresidues within the sequence resulting in a silent change. The HCVpeptides can be, for example, at least 12-704 amino acids in length(e.g., any number between 12-15, 15-20, 20-25, 25-50, 50-100, 100-150,150-250, 250-500 or 500-704 amino acids in length).

Embodiments also include HCV peptides that are substantially identicalto those described above. That is, HCV peptides that have one or moreamino acid residues within SEQ. ID. NOs.: 2-11, 36, and 40-220 andfragments thereof that are substituted by another amino acid of asimilar polarity that acts as a functional equivalent, resulting in asilent alteration. Further, the HCV peptides can have one or more aminoacid residues fused to SEQ. ID. NOs.: 2-11, 36 and SEQ ID NO: 40-220 ora fragment thereof so long as the fusion does not significantly alterthe structure or function (e.g., immunogenic properties) of the HCVpeptide. Substitutes for an amino acid within the sequence can beselected from other members of the class to which the amino acidbelongs. For example, the non-polar (hydrophobic) amino acids includealanine, leucine, isoleucine, valine, proline, phenylalanine,tryptophan, and methionine. The polar neutral amino acids includeglycine, serine, threonine, cysteine, tyrosine, asparagine andglutamine. The positively charged (basic) amino acids include arginine,lysine, and histidine. The negatively charged (acidic) amino acidsinclude aspartic acid and glutamic acid. The aromatic amino acidsinclude phenylalanine, tryptophan, and tyrosine. Accordingly, thepeptide embodiments of the invention are said to be consistingessentially of SEQ. ID. NOs.: 2-27, 36 and SEQ ID NOs: 40-220 in lightof the modifications described above.

The HCV peptides described herein can be prepared by chemical synthesismethods (such as solid phase peptide synthesis) using techniques knownin the art such as those set forth by Merrifield et al., J. Am. Chem.Soc. 85:2149 (1964), Houghten et al., Proc. Natl. Acad. Sci. USA,82:51:32 (1985), Stewart and Young (Solid phase peptide synthesis,Pierce Chem. Co., Rockford, Ill. (1984), and Creighton, 1983, Proteins:Structures and Molecular Principles, W. H. Freeman & Co., N.Y. Suchpolypeptides can be synthesized with or without a methionine on theamino terminus. Chemically synthesized HCV peptides can be oxidizedusing methods set forth in these references to form disulfide bridges.

While the HCV peptides described herein can be chemically synthesized,it can be more effective to produce these polypeptides by recombinantDNA technology. Such methods can be used to construct expression vectorscontaining the HCV nucleotide sequences described above, for example,and appropriate transcriptional and translational control signals. Thesemethods include, for example, in vitro recombinant DNA techniques,synthetic techniques, and in vivo genetic recombination. Alternatively,RNA capable of encoding an HCV nucleotide sequence can be chemicallysynthesized using, for example, synthesizers. See, for example, thetechniques described in Oligonucleotide Synthesis, 1984, Gait, M. J.ed., IRL Press, Oxford. Accordingly, several embodiments concern celllines that have been engineered to express the embodied HCV peptides.For example, some cells are made to express the HCV peptides of SEQ. ID.NOs.: 2-11, 36 and SEQ ID NOs: 40-220 or fragments of these molecules(e.g., SEQ. ID. NOs.: 14-26).

A variety of host-expression vector systems can be utilized to expressthe embodied HCV peptides. Suitable expression systems include, but arenot limited to, microorganisms such as bacteria (e.g., E. coli or B.subtilis) transformed with recombinant bacteriophage DNA, plasmid DNA orcosmid DNA expression vectors containing HCV nucleotide sequences; yeast(e.g., Saccharomyces, Pichia) transformed with recombinant yeastexpression vectors containing the HCV nucleotide sequences; insect cellsystems infected with recombinant virus expression vectors (e.g.,baculovirus) containing the HCV sequences; plant cell systems infectedwith recombinant virus expression vectors (e.g., cauliflower mosaicvirus, CaMV; tobacco mosaic virus, TMV) or transformed with recombinantplasmid expression vectors (e.g., Ti plasmid) containing HCV sequences;or mammalian cell systems (e.g., COS, CHO, BHK, 293, 3T3) harboringrecombinant expression constructs containing promoters derived from thegenome of mammalian cells (e.g., metallothionein promoter) or frommammalian viruses (e.g., the adenovirus late promoter; the vacciniavirus 7.5K promoter).

In bacterial systems, a number of expression vectors can beadvantageously selected depending upon the use intended for the HCV geneproduct being expressed. For example, when a large quantity of such aprotein is to be produced, for the generation of pharmaceuticalcompositions of HCV peptide or for raising antibodies to the HCVpeptide, for example, vectors which direct the expression of high levelsof fusion protein products that are readily purified can be desirable.Such vectors include, but are not limited, to the E. coli expressionvector pUR278 (Ruther et al., EMBO J., 2:1791 (1983), in which the HCVcoding sequence can be ligated individually into the vector in framewith the lacZ coding region so that a fusion protein is produced; pINvectors (Inouye & Inouye, Nucleic Acids Res., 13:3101-3109 (1985); VanHeeke & Schuster, J. Biol. Chem., 264:5503-5509 (1989)); and the like.The pGEX vectors can also be used to express foreign polypeptides asfusion proteins with glutathione S-transferase (GST). In general, suchfusion proteins are soluble and can be purified from lysed cells byadsorption to glutathione-agarose beads followed by elution in thepresence of free glutathione. The PGEX vectors are designed to includethrombin or factor Xa protease cleavage sites so that the cloned targetgene product can be released from the GST moiety.

In an insect system, Autographa californica nuclear polyhedrosis virus(AcNPV) is used as a vector to express foreign genes. The virus grows inSpodoptera frugiperda cells. The HCV coding sequence can be clonedindividually into non-essential regions (for example the polyhedringene) of the virus and placed under control of an AcNPV promoter (forexample the polyhedrin promoter). Successful insertion of an HCV genecoding sequence will result in inactivation of the polyhedrin gene andproduction of non-occluded recombinant virus, (i.e., virus lacking theproteinaceous coat coded for by the polyhedrin gene). These recombinantviruses are then used to infect Spodoptera frugiperda cells in which theinserted gene is expressed. (See e.g., Smith et al., J. Virol. 46: 584(1983); and Smith, U.S. Pat. No. 4,215,051).

In mammalian host cells, a number of viral-based expression systems canbe utilized. In cases where an adenovirus is used as an expressionvector, the HCV nucleotide sequence of interest can be ligated to anadenovirus transcription/translation control complex, e.g., the latepromoter and tripartite leader sequence. This chimeric gene can then beinserted in the adenovirus genome by in vitro or in vivo recombination.Insertion in a non-essential region of the viral genome (e.g., region E1or E3) will result in a recombinant virus that is viable and capable ofexpressing the HCV gene product in infected hosts. (See e.g., Logan &Shenk, Proc. Natl. Acad. Sci. USA 81:3655-3659 (1984)). Specificinitiation signals can also be required for efficient translation ofinserted HCV nucleotide sequences. These signals include the ATGinitiation codon and adjacent sequences.

However, in cases where only a portion of the HCV coding sequence isinserted, exogenous translational control signals, including, perhaps,the ATG initiation codon, can be provided. Furthermore, the initiationcodon can be in phase with the reading frame of the desired codingsequence to ensure translation of the entire insert. These exogenoustranslational control signals and initiation codons can be of a varietyof origins, both natural and synthetic. The efficiency of expression canbe enhanced by the inclusion of appropriate transcription enhancerelements, transcription terminators, etc. (See Bittner et al., Methodsin Enzymol., 153:516-544 (1987)).

In addition, a host cell strain can be chosen, which modulates theexpression of the inserted sequences, or modifies and processes the geneproduct in the specific fashion desired. Such modifications (e.g.,glycosylation) and processing (e.g., cleavage) of protein products areimportant for the function of the protein. Different host cells havecharacteristic and specific mechanisms for the post-translationalprocessing and modification of proteins and gene products. Appropriatecell lines or host systems can be chosen to ensure the correctmodification and processing of the foreign protein expressed. To thisend, eukaryotic host cells that possess the cellular machinery forproper processing of the primary transcript, glycosylation, andphosphorylation of the gene product can be used. Such mammalian hostcells include, but are not limited to, CHO, VERO, BHK, HeLa, COS, MDCK,293, 3T3, and WI38.

For long-term, high-yield production of recombinant proteins, stableexpression is preferred. For example, cell lines that stably express theHCV peptides described above can be engineered. Rather than usingexpression vectors that contain viral origins of replication, host cellscan be transformed with DNA controlled by appropriate expression controlelements (e.g., promoter, enhancer sequences, transcription terminators,polyadenylation sites, etc.), and a selectable marker. Following theintroduction of the foreign DNA, engineered cells are allowed to growfor 1-2 days in an enriched media, and then are switched to a selectivemedia. The selectable marker in the recombinant plasmid confersresistance to the selection and allows cells to stably integrate theplasmid into their chromosomes and grow to form foci which in turn arecloned and expanded into cell lines. This method is advantageously usedto engineer cell lines which express the HCV gene product.

A number of selection systems can be used, including but not limited tothe herpes simplex virus thymidine kinase (Wigler, et al., Cell 11:223(1977), hypoxanthine-guanine phosphoribosyltransferase (Szybalska &Szybalski, Proc. Natl. Acad. Sci. USA 48:2026 (1962)), and adeninephosphoribosyltransferase (Lowy, et al., Cell 22:817 (1980)) genes canbe employed in tk⁻, hgprt⁻ or aprt⁻ cells, respectively. Also,antimetabolite resistance can be used as the basis of selection for thefollowing genes: dhfr, which confers resistance to methotrexate (Wigler,et al., Proc. Natl. Acad. Sci. USA 77:3567 (1980); O'Hare, et al., Proc.Natl. Acad. Sci. USA 78:1527 (1981)); gpt, which confers resistance tomycophenolic acid (Mulligan & Berg, Proc. Natl. Acad. Sci. USA 78:2072(1981)); neo, which confers resistance to the aminoglycoside G-418(Colberre-Garapin, et al., J. Mol. Biol. 150:1 (1981)); and hygro, whichconfers resistance to hygromycin (Santerre, et al., Gene 30:147 (1984)).

Alternatively, any fusion protein can be readily purified by utilizingan antibody specific for the fusion protein being expressed. Forexample, a system described by Janknecht et al. allows for the readypurification of non-denatured fusion proteins expressed in human celllines. (Janknecht, et al., Proc. Natl. Acad. Sci. USA 88: 8972-8976(1991)). In this system, the gene of interest is subcloned into avaccinia recombination plasmid such that the gene's open reading frameis translationally fused to an amino-terminal tag consisting of sixhistidine residues. Extracts from cells infected with recombinantvaccinia virus are loaded onto Ni²⁺ nitriloacetic acid-agarose columnsand histidine-tagged proteins are selectively eluted withimidazole-containing buffers. The example below describes a method thatwas used to express the HCV peptides encoded by the embodied nucleicacids.

Example 13

To characterize NS3/4A-pVAX, MSLF1-pVAX, and the NS3/4A mutantconstructs, described in Example 1, the plasmids were transcribed andtranslated in vitro, and the resulting polypeptides were visualized bysodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Invitro transcription and translation were performed using the T7 coupledreticulocyte lysate system (Promega, Madison, Wis.) according to themanufacturer's instructions. All in vitro translation reactions of theexpression constructs were carried out at 30° C. with ³⁵S-labeledmethionine (Amersham International, Plc, Buckinghamshire, UK). Thelabeled proteins were separated by 12% SDS-PAGE and visualized byexposure to X-ray film (Hyper Film-MP, Amersham) for 6-18 hours.

The in vitro analysis revealed that all proteins were expressed to highamounts from their respective expression constructs. The rNS3 construct(NS3-pVAX vector) produced a single peptide of approximately 61 kDa,whereas, the mutant constructs (e.g., the TGT construct(NS3/4A-TGT-pVAX) and the RGT construct (NS3/4A-RGT-pVAX)) produced asingle polypeptide of approximately 67 kDa, which is identical to themolecular weight of the uncleaved NS3/4A peptide produced from theNS3/4A-pVAX construct. The cleaved product produced from the expressedNS3/4A peptide was approximately 61 kDa, which was identical in size tothe rNS3 produced from the NS3-pVAX vector. These results demonstratedthat the expression constructs were functional, the NS3/4A construct wasenzymatically active, the rNS3 produced a peptide of the predicted size,and the breakpoint mutations completely abolished cleavage at theNS3-NS4A junction.

To compare the translation efficiency from the NS3/4A-pVAX andMSLF1-pVAX plasmids, the amount of input DNA was serially diluted priorto addition to the assay. Serial dilutions of the plasmids revealed thatthe MSLF1 plasmid gave stronger bands at higher dilutions of the plasmidthan the wild-type NS3/4A plasmid, providing evidence that in vitrotranscription and translation was more efficient from the MSLF1 plasmid.The NS3/4A-pVAX and MSLF1 plasmids were then analyzed for proteinexpression using transiently transfected Hep-G2 cells. Similar resultswere obtained in that the MSLF-1 gene provided more efficient expressionof NS3 than the native NS3/4A gene.

The sequences, constructs, vectors, clones, and other materialscomprising the embodied HCV nucleic acids and peptides can be inenriched or isolated form. As used herein, “enriched” means that theconcentration of the material is many times its natural concentration,for example, at least about 2, 5, 10, 100, or 1000 times its naturalconcentration, advantageously 0.01%, by weight, preferably at leastabout 0.1% by weight. Enriched preparations from about 0.5% or more, forexample, 1%, 5%, 10%, and 20% by weight are also contemplated. The term“isolated” requires that the material be removed from its originalenvironment (e.g., the natural environment if it is naturallyoccurring). For example, a naturally-occurring polynucleotide present ina living animal is not isolated, but the same polynucleotide, separatedfrom some or all of the coexisting materials in the natural system, isisolated. It is also advantageous that the sequences be in purifiedform. The term “purified” does not require absolute purity; rather, itis intended as a relative definition. Isolated proteins have beenconventionally purified to electrophoretic homogeneity by Coomassiestaining, for example. Purification of starting material or naturalmaterial to at least one order of magnitude, preferably two or threeorders, and more preferably four or five orders of magnitude isexpressly contemplated.

The HCV gene products described herein can also be expressed in plants,insects, and animals so as to create a transgenic organism. Desirabletransgenic plant systems having an HCV peptide include Arabadopsis,maize, and Chlamydomonas. Desirable insect systems having an HCV peptideinclude, but are not limited to, D. melanogaster and C. elegans. Animalsof any species, including, but not limited to, amphibians, reptiles,birds, mice, hamsters, rats, rabbits, guinea pigs, pigs, micro-pigs,goats, dogs, cats, and non-human primates, e.g., baboons, monkeys, andchimpanzees can be used to generate transgenic animals having anembodied HCV molecule. These transgenic organisms desirably exhibitgermline transfer of HCV peptides described herein.

Any technique known in the art is preferably used to introduce the HCVtransgene into animals to produce the founder lines of transgenicanimals or to knock out or replace existing HCV genes. Such techniquesinclude, but are not limited to pronuclear microinjection (Hoppe, P. C.and Wagner, T. E., 1989, U.S. Pat. No. 4,873,191); retrovirus mediatedgene transfer into germ lines (Van der Putten et al., Proc. Natl. Acad.Sci., USA 82:6148-6152 (1985)); gene targeting in embryonic stem cells(Thompson et al., Cell 56:313-321 (1989)); electroporation of embryos(Lo, Mol. Cell. Biol. 3:1803-1814 (1983); and sperm-mediated genetransfer (Lavitrano et al., Cell 57:717-723 (1989)); see also Gordon,Transgenic Animals, Intl. Rev. Cytol. 115:171-229 (1989).

Following synthesis or expression and isolation or purification of theHCV peptides, the isolated or purified peptide can be used to generateantibodies. Depending on the context, the term “antibodies” canencompass polyclonal, monoclonal, chimeric, single chain, Fab fragmentsand fragments produced by a Fab expression library. Antibodies thatrecognize the HCV peptides have many uses including, but not limited to,biotechnological applications, therapeutic/prophylactic applications,and diagnostic applications.

For the production of antibodies, various hosts including goats,rabbits, rats, mice, and humans etc. can be immunized by injection withan HCV peptide. Depending on the host species, various adjuvants can beused to increase immunological response. Such adjuvants include, but arenot limited to, ribavirin, Freund's, mineral gels such as aluminumhydroxide, and surface active substances such as lysolecithin, pluronicpolyols, polyanions, peptides, oil emulsions, keyhole limpet hemocyanin,and dinitrophenol. BCG (Bacillus Calmette-Guerin) and Corynebacteriumparvum are also potentially useful adjuvants.

Peptides used to induce specific antibodies can have an amino acidsequence consisting of at least four amino acids, and preferably atleast 10 to 15 amino acids. By one approach, short stretches of aminoacids encoding fragments of NS3/4A are fused with those of anotherprotein such as keyhole limpet hemocyanin such that an antibody isproduced against the chimeric molecule. Additionally, a compositioncomprising ribavirin and an HCV peptide (SEQ. ID. NOs.: 2-11, 40-220 andSEQ. ID. NO.: 36), a fragment thereof containing any number ofconsecutive amino acids between at least 3-50 (e.g., 3, 4, 6, 8, 10, 12,15, 20, 25, 30, 35, 40, 45, or 50 amino acids) (e.g., SEQ. ID. NOs.:4-26), or a nucleic acid encoding one or more of these molecules isadministered to an animal, preferably a mammal including a human. Whileantibodies capable of specifically recognizing HCV can be generated byinjecting synthetic 3-mer, 10-mer, and 15-mer peptides that correspondto an HCV peptide into mice, a more diverse set of antibodies can begenerated by using recombinant HCV peptides, prepared as describedabove.

To generate antibodies to an HCV peptide, substantially pure peptide isisolated from a transfected or transformed cell. The concentration ofthe peptide in the final preparation is adjusted, for example, byconcentration on an Amicon filter device, to the level of a fewmicrograms/ml. Monoclonal or polyclonal antibody to the peptide ofinterest can then be prepared as follows:

Monoclonal antibodies to an HCV peptide can be prepared using anytechnique that provides for the production of antibody molecules bycontinuous cell lines in culture. These include, but are not limited to,the hybridoma technique originally described by Koehler and Milstein(Nature 256:495-497 (1975)), the human B-cell hybridoma technique(Kosbor et al. Immunol Today 4:72 (1983)); Cote et al Proc Natl Acad Sci80:2026-2030 (1983), and the EBV-hybridoma technique Cole et al.Monoclonal Antibodies and Cancer Therapy, Alan R. Liss Inc, New YorkN.Y., pp 77-96 (1985). In addition, techniques developed for theproduction of “chimeric antibodies”, the splicing of mouse antibodygenes to human antibody genes to obtain a molecule with appropriateantigen specificity and biological activity can be used. (Morrison etal. Proc Natl Acad Sci 81:6851-6855 (1984); Neuberger et al. Nature312:604-608 (1984); Takeda et al. Nature 314:452-454 (1985)).Alternatively, techniques described for the production of single chainantibodies (U.S. Pat. No. 4,946,778) can be adapted to produceHCV-specific single chain antibodies. Antibodies can also be produced byinducing in vivo production in the lymphocyte population or by screeningrecombinant immunoglobulin libraries or panels of highly specificbinding reagents as disclosed in Orlandi et al., Proc Natl Acad Sci 86:3833-3837 (1989), and Winter G. and Milstein C; Nature 349:293-299(1991).

Antibody fragments that contain specific binding sites for an HCVpeptide can also be generated. For example, such fragments include, butare not limited to, the F(ab′)₂ fragments that can be produced by pepsindigestion of the antibody molecule and the Fab fragments that can begenerated by reducing the disulfide bridges of the F(ab′)₂ fragments.Alternatively, Fab expression libraries can be constructed to allowrapid and easy identification of monoclonal Fab fragments with thedesired specificity. (Huse W. D. et al. Science 256:1275-1281 (1989)).

By one approach, monoclonal antibodies to an HCV peptide are made asfollows. Briefly, a mouse is repetitively inoculated with a fewmicrograms of the selected protein or peptides derived therefrom over aperiod of a few weeks. The mouse is then sacrificed, and the antibodyproducing cells of the spleen isolated. The spleen cells are fused inthe presence of polyethylene glycol with mouse myeloma cells, and theexcess unfused cells destroyed by growth of the system on selectivemedia comprising aminopterin (HAT media). The successfully fused cellsare diluted and aliquots of the dilution placed in wells of a microtiterplate where growth of the culture is continued. Antibody-producingclones are identified by detection of antibody in the supernatant fluidof the wells by immunoassay procedures, such as ELISA, as originallydescribed by Engvall, E., Meth. Enzymol. 70:419 (1980), and derivativemethods thereof. Selected positive clones can be expanded and theirmonoclonal antibody product harvested for use. Detailed procedures formonoclonal antibody production are described in Davis, L. et al. BasicMethods in Molecular Biology Elsevier, New York. Section 21-2.

Polyclonal antiserum containing antibodies to heterogeneous epitopes ofa single protein can be prepared by immunizing suitable animals with theexpressed protein or peptides derived therefrom described above, whichcan be unmodified or modified to enhance immunogenicity. Effectivepolyclonal antibody production is affected by many factors related bothto the antigen and the host species. For example, small molecules tendto be less immunogenic than others and can require the use of carriersand adjuvant. Also, host animals vary in response to site ofinoculations and dose, with both inadequate or excessive doses ofantigen resulting in low titer antisera. Small doses (ng level) ofantigen administered at multiple intradermal sites appears to be mostreliable. An effective immunization protocol for rabbits can be found inVaitukaitis, J. et al. J. Clin. Endocrinol. Metab. 33:988-991 (1971).

Booster injections are given at regular intervals, and antiserumharvested when antibody titer thereof, as determinedsemi-quantitatively, for example, by double immunodiffusion in agaragainst known concentrations of the antigen, begins to fall. See, forexample, Ouchterlony, O. et al., Chap. 19 in: Handbook of ExperimentalImmunology D. Wier (ed) Blackwell (1973). Plateau concentration ofantibody is usually in the range of 0.1 to 0.2 mg/ml of serum (about 12μM). Affinity of the antisera for the antigen is determined by preparingcompetitive binding curves, as described, for example, by Fisher, D.,Chap. 42 in: Manual of Clinical Immunology, 2d Ed. (Rose and Friedman,Eds.) Amer. Soc. For Microbiol., Washington, D.C. (1980). Antibodypreparations prepared according to either protocol are useful inquantitative immunoassays that determine concentrations ofantigen-bearing substances in biological samples; they are also usedsemi-quantitatively or qualitatively (e.g., in diagnostic embodimentsthat identify the presence of HCV in biological samples). The nextsection describes how some of the novel nucleic acids and peptidesdescribed above can be used in diagnostics.

Diagnostic Embodiments

Generally, the embodied diagnostics are classified according to whethera nucleic acid or protein-based assay is used. Some diagnostic assaysdetect the presence or absence of an embodied HCV nucleic acid sequencein a sample obtained from a patient, whereas, other assays seek toidentify whether an embodied HCV peptide is present in a biologicalsample obtained from a patient. Additionally, the manufacture of kitsthat incorporate the reagents and methods described herein that allowfor the rapid detection and identification of HCV are also embodied.These diagnostic kits can include, for example, an embodied nucleic acidprobe or antibody, which specifically detects HCV. The detectioncomponent of these kits will typically be supplied in combination withone or more of the following reagents. A support capable of absorbing orotherwise binding DNA, RNA, or protein will often be supplied. Availablesupports include membranes of nitrocellulose, nylon or derivatized nylonthat can be characterized by bearing an array of positively chargedsubstituents. One or more restriction enzymes, control reagents,buffers, amplification enzymes, and non-human polynucleotides likecalf-thymus or salmon-sperm DNA can be supplied in these kits.

Useful nucleic acid-based diagnostics include, but are not limited to,direct DNA sequencing, Southern Blot analysis, dot blot analysis,nucleic acid amplification, and combinations of these approaches. Thestarting point for these analysis is isolated or purified nucleic acidfrom a biological sample obtained from a patient suspected ofcontracting HCV or a patient at risk of contracting HCV. The nucleicacid is extracted from the sample and can be amplified by RT-PCR and/orDNA amplification using primers that correspond to regions flanking theembodied HCV nucleic acid sequences (e.g., NS3/4A (SEQ. ID. NO.: 1)).

In some embodiments, nucleic acid probes that specifically hybridizewith HCV sequences are attached to a support in an ordered array,wherein the nucleic acid probes are attached to distinct regions of thesupport that do not overlap with each other. Preferably, such an orderedarray is designed to be “addressable” where the distinct locations ofthe probe are recorded and can be accessed as part of an assayprocedure. These probes are joined to a support in different knownlocations. The knowledge of the precise location of each nucleic acidprobe makes these “addressable” arrays particularly useful in bindingassays. The nucleic acids from a preparation of several biologicalsamples are then labeled by conventional approaches (e.g., radioactivityor fluorescence) and the labeled samples are applied to the array underconditions that permit hybridization.

If a nucleic acid in the samples hybridizes to a probe on the array,then a signal will be detected at a position on the support thatcorresponds to the location of the hybrid. Since the identity of eachlabeled sample is known and the region of the support on which thelabeled sample was applied is known, an identification of the presenceof the polymorphic variant can be rapidly determined. These approachesare easily automated using technology known to those of skill in the artof high throughput diagnostic or detection analysis.

Additionally, an approach opposite to that presented above can beemployed. Nucleic acids present in biological samples can be disposed ona support so as to create an addressable array. Preferably, the samplesare disposed on the support at known positions that do not overlap. Thepresence of HCV nucleic acids in each sample is determined by applyinglabeled nucleic acid probes that complement nucleic acids, which encodeHCV peptides, at locations on the array that correspond to the positionsat which the biological samples were disposed. Because the identity ofthe biological sample and its position on the array is known, theidentification of a patient that has been infected with HCV can berapidly determined. These approaches are also easily automated usingtechnology known to those of skill in the art of high throughputdiagnostic analysis.

Any addressable array technology known in the art can be employed. Oneparticular embodiment of polynucleotide arrays is known as Genechips™,and has been generally described in U.S. Pat. No. 5,143,854; PCTpublications WO 90/15070 and 92/10092. These arrays are generallyproduced using mechanical synthesis methods or light directed synthesismethods, which incorporate a combination of photolithographic methodsand solid phase oligonucleotide synthesis. (Fodor et al., Science,251:767-777, (1991)). The immobilization of arrays of oligonucleotideson solid supports has been rendered possible by the development of atechnology generally identified as “Very Large Scale Immobilized PolymerSynthesis” (VLSPIS™) in which, typically, probes are immobilized in ahigh density array on a solid surface of a chip. Examples of VLSPIS™technologies are provided in U.S. Pat. Nos. 5,143,854 and 5,412,087 andin PCT Publications WO 90/15070, WO 92/10092 and WO 95/11995, whichdescribe methods for forming oligonucleotide arrays through techniquessuch as light-directed synthesis techniques. In designing strategiesaimed at providing arrays of nucleotides immobilized on solid supports,further presentation strategies were developed to order and display theoligonucleotide arrays on the chips in an attempt to maximizehybridization patterns and diagnostic information. Examples of suchpresentation strategies are disclosed in PCT Publications WO 94/12305,WO 94/11530, WO 97/29212, and WO 97/31256.

A wide variety of labels and conjugation techniques are known by thoseskilled in the art and can be used in various nucleic acid assays. Thereare several ways to produce labeled nucleic acids for hybridization orPCR including, but not limited to, oligolabeling, nick translation,end-labeling, or PCR amplification using a labeled nucleotide.Alternatively, a nucleic acid encoding an HCV peptide can be cloned intoa vector for the production of an mRNA probe. Such vectors are known inthe art, are commercially available, and can be used to synthesize RNAprobes in vitro by addition of an appropriate RNA polymerase such as T7,T3 or SP6 and labeled nucleotides. A number of companies such asPharmacia Biotech (Piscataway N.J.), Promega (Madison Wis.), and U.S.Biochemical Corp (Cleveland Ohio) supply commercial kits and protocolsfor these procedures. Suitable reporter molecules or labels includethose radionuclides, enzymes, fluorescent, chemiluminescent, orchromogenic agents, as well as, substrates, cofactors, inhibitors,magnetic particles and the like.

The presence of an HCV peptide in a protein sample obtained from apatient can also be detected by using conventional assays and theembodiments described herein. For example, antibodies that areimmunoreactive with the disclosed HCV peptides can be used to screenbiological samples for the presence of HCV infection. In preferredembodiments, antibodies that are reactive to the embodied HCV peptidesare used to immunoprecipitate the disclosed HCV peptides from biologicalsamples or are used to react with proteins obtained from a biologicalsample on Western or Immunoblots. Favored diagnostic embodiments alsoinclude enzyme-linked immunosorbant assays (ELISA), radioimmunoassays(RIA), immunoradiometric assays (IRMA) and immunoenzymatic assays(IEMA), including sandwich assays using monoclonal and/or polyclonalantibodies specific for the disclosed HCV peptides. Exemplary sandwichassays are described by David et al., in U.S. Pat. Nos. 4,376,110 and4,486,530. Other embodiments employ aspects of the immune-striptechnology disclosed in U.S. Pat. Nos. 5,290,678; 5,604,105; 5,710,008;5,744,358; and 5,747,274.

In another preferred protein-based diagnostic, the antibodies describedherein are attached to a support in an ordered array, wherein aplurality of antibodies are attached to distinct regions of the supportthat do not overlap with each other. As with the nucleic acid-basedarrays, the protein-based arrays are ordered arrays that are designed tobe “addressable” such that the distinct locations are recorded and canbe accessed as part of an assay procedure. These probes are joined to asupport in different known locations. The knowledge of the preciselocation of each probe makes these “addressable” arrays particularlyuseful in binding assays. For example, an addressable array can comprisea support having several regions to which are joined a plurality ofantibody probes that specifically recognize HCV peptides present in abiological sample and differentiate the isotype of HCV identifiedherein.

By one approach, proteins are obtained from biological samples and arethen labeled by conventional approaches (e.g., radioactivity,colorimetrically, or fluorescently). The labeled samples are thenapplied to the array under conditions that permit binding. If a proteinin the sample binds to an antibody probe on the array, then a signalwill be detected at a position on the support that corresponds to thelocation of the antibody-protein complex. Since the identity of eachlabeled sample is known and the region of the support on which thelabeled sample was applied is known, an identification of the presence,concentration, and/or expression level can be rapidly determined. Thatis, by employing labeled standards of a known concentration of HCVpeptide, an investigator can accurately determine the proteinconcentration of the particular peptide in a tested sample and can alsoassess the expression level of the HCV peptide. Conventional methods indensitometry can also be used to more accurately determine theconcentration or expression level of the HCV peptide. These approachesare easily automated using technology known to those of skill in the artof high throughput diagnostic analysis.

In another embodiment, an approach opposite to that presented above canbe employed. Proteins present in biological samples can be disposed on asupport so as to create an addressable array. Preferably, the proteinsamples are disposed on the support at known positions that do notoverlap. The presence of an HCV peptide in each sample is thendetermined by applying labeled antibody probes that recognize epitopesspecific for the HCV peptide. Because the identity of the biologicalsample and its position on the array is known, an identification of thepresence, concentration, and/or expression level of an HCV peptide canbe rapidly determined.

That is, by employing labeled standards of a known concentration of HCVpeptide, an investigator can accurately determine the concentration ofpeptide in a sample and from this information can assess the expressionlevel of the peptide. Conventional methods in densitometry can also beused to more accurately determine the concentration or expression levelof the HCV peptide. These approaches are also easily automated usingtechnology known to those of skill in the art of high throughputdiagnostic analysis. As detailed above, any addressable array technologyknown in the art can be employed. The next section describes morecompositions that include the HCV nucleic acids and/or HCV peptidesdescribed herein.

Compositions Comprising HCV Nucleic Acids or Peptides

Embodiments of the invention also include NS3/4A fusion proteins ornucleic acids encoding these molecules. For instance, production andpurification of recombinant protein may be facilitated by the additionof auxiliary amino acids to form a “tag”. Such tags include, but are notlimited to, His-6, Flag, Myc and GST. The tags may be added to theC-terminus, N-terminus, or within the NS3/4A amino acid sequence.Further embodiments include NS3/4A fusion proteins with amino or carboxyterminal truncations, or internal deletions, or with additionalpolypeptide sequences added to the amino or carboxy terminal ends, oradded internally. Other embodiments include NS3/4A fusion proteins, ortruncated or mutated versions thereof, where the residues of the NS3/4Aproteolytic cleavage site have been substituted. Such substitutionsinclude, but are not limited to, sequences where the P1′ site is a Ser,Gly, or Pro, or the P1 position is an Arg, or where the P8 to P4′sequence is Ser-Ala-Asp-Leu-Glu-Val-Val-Thr-Ser-Thr-Trp-Val (SEQ. ID.NO.: 15).

More embodiments concern an immunogen comprising the NS3/4A fusionprotein, or a truncated, mutated, or modified version thereof, capableof eliciting an enhanced immune response against NS3. The immunogen canbe provided in a substantially purified form, which means that theimmunogen has been rendered substantially free of other proteins,lipids, carbohydrates or other compounds with which it naturallyassociates.

Some embodiments contain at least one of the HCV nucleic acids or HCVpeptides (e.g., SEQ. ID. NOs.: 1-27, 35, 36 or 40-220) joined to asupport. Preferably, these supports are manufactured so as to create amultimeric agent. These multimeric agents provide the HCV peptide ornucleic acid in such a form or in such a way that a sufficient affinityto the molecule is achieved. A multimeric agent having an HCV nucleicacid or peptide can be obtained by joining the desired molecule to amacromolecular support. A “support” can be a termed a carrier, aprotein, a resin, a cell membrane, a capsid or portion thereof, or anymacromolecular structure used to join or immobilize such molecules.Solid supports include, but are not limited to, the walls of wells of areaction tray, test tubes, polystyrene beads, magnetic beads,nitrocellulose strips, membranes, microparticles such as latexparticles, animal cells, Duracyte®, artificial cells, and others. An HCVnucleic acid or peptide can also be joined to inorganic carriers, suchas silicon oxide material (e.g., silica gel, zeolite, diatomaceous earthor aminated glass) by, for example, a covalent linkage through ahydroxy, carboxy or amino group and a reactive group on the carrier.

In several multimeric agents, the macromolecular support has ahydrophobic surface that interacts with a portion of the HCV nucleicacid or peptide by a hydrophobic non-covalent interaction. In somecases, the hydrophobic surface of the support is a polymer such asplastic or any other polymer in which hydrophobic groups have beenlinked such as polystyrene, polyethylene or polyvinyl. Additionally, HCVnucleic acid or peptide can be covalently bound to carriers includingproteins and oligo/polysaccarides (e.g. cellulose, starch, glycogen,chitosan or aminated sepharose). In these later multimeric agents, areactive group on the molecule, such as a hydroxy or an amino group, isused to join to a reactive group on the carrier so as to create thecovalent bond. Additional multimeric agents comprise a support that hasother reactive groups that are chemically activated so as to attach theHCV nucleic acid or peptide. For example, cyanogen bromide activatedmatrices, epoxy activated matrices, thio and thiopropyl gels,nitrophenyl chloroformate and N-hydroxy succinimide chlorformatelinkages, or oxirane acrylic supports are used. (Sigma).

Carriers for use in the body, (i.e. for prophylactic or therapeuticapplications) are desirably physiological, non-toxic and preferably,non-immunoresponsive. Suitable carriers for use in the body includepoly-L-lysine, poly-D, L-alanine, liposomes, capsids that display thedesired HCV peptide or nucleic acid, and Chromosorb® (Johns-ManvilleProducts, Denver Co.). Ligand conjugated Chromosorb® (Synsorb-Pk) hasbeen tested in humans for the prevention of hemolytic-uremic syndromeand was reported as not presenting adverse reactions. (Armstrong et al.J. Infectious Diseases 171:1042-1045 (1995)). For some embodiments, a“naked” carrier (i.e., lacking an attached HCV nucleic acid or peptide)that has the capacity to attach an HCV nucleic acid or peptide in thebody of a organism is administered. By this approach, a “prodrug-type”therapy is envisioned in which the naked carrier is administeredseparately from the HCV nucleic acid or peptide and, once both are inthe body of the organism, the carrier and the HCV nucleic acid orpeptide are assembled into a multimeric complex.

The insertion of linkers, (e.g., “λ linkers” engineered to resemble theflexible regions of λ phage) of an appropriate length between the HCVnucleic acid or peptide and the support are also contemplated so as toencourage greater flexibility of the HCV peptide, hybrid, or bindingpartner and thereby overcome any steric hindrance that can be presentedby the support. The determination of an appropriate length of linkerthat allows for an optimal cellular response or lack thereof, can bedetermined by screening the HCV nucleic acid or peptide with varyinglinkers in the assays detailed in the present disclosure.

A composite support comprising more than one type of HCV nucleic acid orpeptide is also envisioned. A “composite support” can be a carrier, aresin, or any macromolecular structure used to attach or immobilize twoor more different HCV nucleic acids or peptides. As above, the insertionof linkers, such as λ linkers, of an appropriate length between the HCVnucleic acid or peptide and the support is also contemplated so as toencourage greater flexibility in the molecule and thereby overcome anysteric hindrance that can occur. The determination of an appropriatelength of linker that allows for an optimal cellular response or lackthereof, can be determined by screening the HCV nucleic acid or peptidewith varying linkers in the assays detailed in the present disclosure.

In other embodiments, the multimeric and composite supports discussedabove can have attached multimerized HCV nucleic acids or peptides so asto create a “multimerized-multimeric support” and a“multimerized-composite support”, respectively. A multimerized ligandcan, for example, be obtained by coupling two or more HCV nucleic acidsor peptides in tandem using conventional techniques in molecularbiology. The multimerized form of the HCV nucleic acid or peptide can beadvantageous for many applications because of the ability to obtain anagent with a higher affinity, for example. The incorporation of linkersor spacers, such as flexible λ linkers, between the individual domainsthat make-up the multimerized agent can also be advantageous for someembodiments. The insertion of λ linkers of an appropriate length betweenprotein binding domains, for example, can encourage greater flexibilityin the molecule and can overcome steric hindrance. Similarly, theinsertion of linkers between the multimerized HCV nucleic acid orpeptide and the support can encourage greater flexibility and limitsteric hindrance presented by the support. The determination of anappropriate length of linker can be determined by screening the HCVnucleic acids or peptides in the assays detailed in this disclosure.

Embodiments also include vaccine compositions and immunogen preparationscomprising the NS3/4A fusion protein, or a truncated or mutated versionthereof, and, optionally, an adjuvant. The next section describes someof these compositions in greater detail.

Vaccine Compositions and Immunogenic Preparations

Vaccine compositions and immunogenic preparations comprising, consistingof, or consisting essentially of either an embodied nucleic acidencoding a chimeric NS3/4A peptide or a chimeric NS3/4A polypeptide, orboth, are contemplated. These compositions typically contain anadjuvant, but do not necessarily require an adjuvant. That is many ofthe nucleic acids and peptides described herein function as immunogenswhen administered neat. The compositions described herein (e.g., theNS3/4A chimeric immunogens and vaccine compositions containing anadjuvant, such as ribavirin) can be manufactured in accordance withconventional methods of galenic pharmacy to produce medicinal agents foradministration to animals, e.g., mammals including humans. (See, e.g.,U.S. Pat. Nos. 6,680,059 and 6,858,590, hereby expressly incorporated byreference in their entireties).

Various nucleic acid-based vaccines are known and it is contemplatedthat these compositions and approaches to immunotherapy can be augmentedby reformulation with ribavirin (See, e.g., U.S. Pat. Nos. 5,589,466 and6,235,888, hereby expressly incorporated by reference in theirentireties). By one approach, for example, a gene encoding one of theNS3/4A chimeric polypeptides described herein is cloned into anexpression vector capable of expressing the polypeptide when introducedinto a subject. The expression construct is introduced into the subjectin a mixture of adjuvant (e.g., ribavirin) or in conjunction with anadjuvant (e.g., ribavirin). For example, the adjuvant (e.g., ribavirin)is administered shortly after the expression construct at the same site.Alternatively, RNA encoding the NS3/4A chimeric polypeptide of interestis provided to the subject in a mixture with ribavirin or in conjunctionwith an adjuvant (e.g., ribavirin).

Where the antigen is to be DNA (e.g., preparation of a DNA vaccinecomposition), suitable promoters include Simian Virus 40 (SV40), MouseMammary Tumor Virus (MMTV) promoter, Human Immunodeficiency Virus (HIV)such as the HIV Long Terminal Repeat (LTR) promoter, Moloney virus, ALV,Cytomegalovirus (CMV) such as the CMV immediate early promoter, EpsteinBarr Virus (EBV), Rous Sarcoma Virus (RSV) as well as promoters fromhuman genes such as human actin, human myosin, human hemoglobin, humanmuscle creatine and human metallothionein can be used. Examples ofpolyadenylation signals useful with some embodiments, especially in theproduction of a genetic vaccine for humans, include but are not limitedto, SV40 polyadenylation signals and LTR polyadenylation signals. Inparticular, the SV40 polyadenylation signal, which is in pCEP4 plasmid(Invitrogen, San Diego Calif.), referred to as the SV40 polyadenylationsignal, is used.

In addition to the regulatory elements required for gene expression,other elements may also be included in a gene construct. Such additionalelements include enhancers. The enhancer may be selected from the groupincluding but not limited to: human actin, human myosin, humanhemoglobin, human muscle creatine and viral enhancers such as those fromCMV, RSV and EBV. Gene constructs can be provided with mammalian originof replication in order to maintain the construct extrachromosomally andproduce multiple copies of the construct in the cell. Plasmids pCEP4 andpREP4 from Invitrogen (San Diego, Calif.) contain the Epstein Barr virusorigin of replication and nuclear antigen EBNA-1 coding region, whichproduces high copy episomal replication without integration. All formsof DNA, whether replicating or non-replicating, which do not becomeintegrated into the genome, and which are expressible, can be used.Preferably, the genetic vaccines comprise ribavirin and a nucleic acidencoding a NS3/4A polypeptide.

More embodiments concern an immunogen comprising the chimeric NS3/4Apolypeptide, or a truncated, mutated, or modified version thereof,capable of eliciting an enhanced immune response against a targetantigen. The immunogen can be provided in a substantially purified form,which means that the immunogen has been rendered substantially free ofother proteins, lipids, carbohydrates or other compounds with which itnaturally associates.

Some embodiments contain at least one of the nucleic acids describedjoined to a support. Preferably, these supports are manufactured so asto create a multimeric agent. These multimeric agents provide thechimeric NS3/4A chimeric polypeptide or encoding nucleic acid in such aform or in such a way that a sufficient affinity to the molecule isachieved. A multimeric agent having a chimeric NS3/4A chimericpolypeptide or encoding nucleic acid can be obtained by joining thedesired molecule to a macromolecular support. A “support” can be atermed a carrier, a protein, a resin, a cell membrane, a capsid orportion thereof, or any macromolecular structure used to join orimmobilize such molecules. Solid supports include, but are not limitedto, the walls of wells of a reaction tray, test tubes, polystyrenebeads, magnetic beads, nitrocellulose strips, membranes, microparticlessuch as latex particles, animal cells, DURACYTE®, artificial cells, andothers. A chimeric NS3/4A polypeptide or encoding nucleic acid can alsobe joined to inorganic carriers, such as silicon oxide material (e.g.,silica gel, zeolite, diatomaceous earth or aminated glass) by, forexample, a covalent linkage through a hydroxy, carboxy or amino groupand a reactive group on the carrier.

In several multimeric agents, the macromolecular support has ahydrophobic surface that interacts with a portion of the chimeric NS3/4Achimeric polypeptide or encoding nucleic acid by a hydrophobicnon-covalent interaction. In some cases, the hydrophobic surface of thesupport is a polymer such as plastic or any other polymer in whichhydrophobic groups have been linked such as polystyrene, polyethylene orpolyvinyl. Additionally, chimeric NS3/4A polypeptides or encodingnucleic acids can be covalently bound to carriers including proteins andoligo/polysaccharides (e.g. cellulose, starch, glycogen, chitosane,aminated sepharose, or the gal epitope (e.g., gal-α-1, 3 gal-β). Inthese later multimeric agents, a reactive group on the molecule, such asa hydroxy or an amino group, is used to join to a reactive group on thecarrier so as to create the covalent bond. Additional multimeric agentscomprise a support that has other reactive groups that are chemicallyactivated so as to attach chimeric NS3/4A polypeptides or encodingnucleic acids. For example, cyanogen bromide activated matrices, epoxyactivated matrices, thio and thiopropyl gels, nitrophenyl chloroformateand N-hydroxy succinimide chlorformate linkages, or oxirane acrylicsupports are used. (Sigma).

Carriers for use in the body, (i.e. for prophylactic or therapeuticapplications) are desirably physiological, non-toxic and preferably,non-immunoresponsive. Suitable carriers for use in the body includepoly-L-lysine, poly-D, L-alanine, liposomes, capsids that display thedesired NS3/4A chimeric peptide or nucleic acid, and CHROMSORB®(Johns-Manville Products, Denver Co.). Ligand conjugated CHROMSORB®(Synsorb-Pk) has been tested in humans for the prevention ofhemolytic-uremic syndrome and was reported as not presenting adversereactions. (Armstrong et al. J. Infectious Diseases 171:1042-1045(1995)). For some embodiments, a “naked” carrier (i.e., lacking anattached chimeric NS3/4A chimeric polypeptides or encoding nucleicacids) that has the capacity to attach a chimeric NS3/4A chimericpolypeptide or encoding nucleic acid in the body of a organism isadministered. By this approach, a “prodrug-type” therapy is envisionedin which the naked carrier is administered separately from the NS3/4Achimeric polypeptide or encoding nucleic acid and, once both are in thebody of the organism, the carrier and NS3/4A chimeric polypeptide orencoding nucleic acid are assembled into a multimeric complex.

The insertion of linkers of an appropriate length between the NS3/4Achimeric polypeptide or encoding nucleic acid and the support are alsocontemplated so as to encourage greater flexibility of the NS3/4Achimeric polypeptide, encoding nucleic acid, hybrid, or binding partnerand thereby overcome any steric hindrance that can be presented by thesupport. The determination of an appropriate length of linker thatallows for an optimal cellular response or lack thereof, can bedetermined by screening the NS3/4A chimeric polypeptide or encodingnucleic acid with varying linkers in the assays detailed in the presentdisclosure.

A composite support comprising more than one type of NS3/4A chimericpolypeptide or encoding nucleic acid is also envisioned. A “compositesupport” can be a carrier, a resin, or any macromolecular structure usedto attach or immobilize two or more different NS3/4A chimericpolypeptides or encoding nucleic acids. As above, the insertion oflinkers, such as λ linkers, of an appropriate length between the NS3/4Achimeric polypeptide or encoding nucleic acid and the support is alsocontemplated so as to encourage greater flexibility in the molecule andthereby overcome any steric hindrance that can occur. The determinationof an appropriate length of linker that allows for an optimal cellularresponse or lack thereof, can be determined by screening the NS3/4Achimeric polypeptide or encoding nucleic acid with varying linkers inthe assays detailed in the present disclosure.

In other embodiments, the multimeric and composite supports discussedabove can have attached multimerized NS3/4A chimeric polypeptides orencoding nucleic acids so as to create a “multimerized-multimericsupport” and a “multimerized-composite support”, respectively. Amultimerized ligand can, for example, be obtained by coupling two ormore NS3/4A chimeric polypeptides or encoding nucleic acids in tandemusing conventional techniques in molecular biology. The multimerizedform of NS3/4A chimeric polypeptides or encoding nucleic acids can beadvantageous for many applications because of the ability to obtain anagent with a higher affinity, for example. The incorporation of linkerssuch as flexible λ linkers, between the individual domains that make-upthe multimerized agent can also be advantageous for some embodiments.The insertion of λ linkers of an appropriate length between proteinbinding domains, for example, can encourage greater flexibility in themolecule and can overcome steric hindrance. Similarly, the insertion oflinkers between the multimerized NS3/4A chimeric polypeptides orencoding nucleic acids and the support can encourage greater flexibilityand limit steric hindrance presented by the support. The determinationof an appropriate length of linker can be determined by screening theNS3/4A chimeric polypeptides or encoding nucleic acid in the assaysdetailed in this disclosure.

Aspects of the present invention also relate to a modified hepatitis Cvirus (HCV) NS3/4A protein that is linked to a pendent hapten (e.g., a Tcell epitope) through chemically-reactive amino acid residue, which maybe, optionally, inserted into or attached to (e.g., a linker on eitherthe N terminal or C terminal end) the NS3/4A sequence. Such anintroduced or already present chemically-reactive amino acid residue ischaracterized in that it has a chemically-reactive side chain thatprovides a chemical group for pendently linking the NS3/4A polypeptideto the hapten. Typically, the chemically-reactive amino acid residue isa lysine, cysteine, or histidine residue or a carboxyl-containingresidue such as aspartic acid or glutamic acid, preferably lysine or acarboxyl-containing residue, and most preferably lysine. The haptenbonded to the chemically-reactive amino acid residue is any compound ofinterest for generating an immune response, and is typically a T cellepitope. Preferably, the hapten is a polypeptide hapten, a carbohydratehapten, or a non-peptidal/non-saccharidal (chemical) hapten. In someembodiments, the hapten is a pathogen-related hapten, for example, a Tcell epitope provided herein. The word “hapten” is used in this contextto describe molecules that are capable of stimulating an immune response(e.g., production of antibody) when chemically coupled to NS3/4A. Theword is often used for small nonantigenic molecules in the art, butherein, it merely refers to the molecule that is to be pendently linkedto NS3/4A, even if it is antigenic or not small. The chemically-reactiveamino acid residue can be at any position within the epitope and NS3/4Apolypeptide or attached to either end of these molecules (N terminal orC terminal). As stated above, the introduced chemically-reactive aminoacid residue has a chemically-reactive side chain that provides afunctional group for derivatizing the NS3/4A polypeptide (e.g.,conjugating a T cell epitope to the NS3/4A). Useful side chainfunctional groups include epsilon-amino groups, beta- or gamma-carboxylgroups, thiol (—SH) groups and aromatic rings (e.g. tyrosine andhistidine). The chemically-reactive amino acid residue is typically alysine, cysteine, or histidine residue or a carboxyl-containing residuesuch as aspartic acid or glutamic acid. Lysine is a particularlypreferred chemically-reactive amino acid residue. In addition of the useof an individual chemically-reactive amino acid residue in the insertsuch as aspartic acid or lysine, substantially any sequence of thedesired length that contains a chemically-reactive amino acid residuecan be used.

Any hapten against which antibody production is desired can be linked toan NS3/4A peptide or fragment thereof, as described herein, to form animmunogenic composition. The hapten of interest typically is T cellepitope. The hapten can be a polypeptide, a carbohydrate (saccharide),or a non-polypeptide, non-carbohydrate chemical such as2,4-dinitrobenzene, however.

Methods for operatively linking individual haptens to a protein orpolypeptide through an amino acid residue side chain of the protein orpolypeptide to form a pendently-linked immunogenic conjugate, e.g., abranched-chain polypeptide polymer, are well known in the art. Thosemethods include linking through one or more types of functional groupson various side chains and result in the carrier protein polypeptidebackbone being pendently linked-covalently linked (coupled) to thehapten but separated by at least one side chain.

Methods for linking carrier proteins to haptens using each of the abovefunctional groups are described in Erlanger, Method of Enzymology, 70:85(1980), Aurameas, et al., Scand. J. Immunol., Vol. 8, Suppl. 7, 7-23(1978) and U.S. Pat. No. 4,493,795 to Nestor et al., all of which arehereby expressly incorporated by reference in their entireties. Inaddition, a site-directed coupling reaction, as described in Rodwell etal., Biotech., 3, 889-894 (1985), herein expressly incorporated byreference in its entirety, can be carried out so that the biologicalactivity of the polypeptides is not substantially diminished.

Furthermore, as is well known in the art, both the NS3/4A protein orfragment thereof and a polypeptide hapten can be used in their nativeform or their functional group content can be modified by succinylationof lysine residues or reaction with cysteine-thiolactone. A sulfhydrylgroup can also be incorporated into either molecule by reaction of aminofunctions with 2-iminothiolane or the N-hydroxysuccinimide ester of3-(3-dithiopyridyl)propionate.

The NS3/4A peptide or fragment thereof or hapten can also be modified toincorporate a spacer arm, such as hexamethylene diamine or otherbifunctional molecules of similar size, to facilitate the pendentlinking.

Methods for covalent bonding of a polypeptide hapten are extremelyvaried and are well known by workers skilled in the immunological arts.For example, following U.S. Pat. No. 4,818,527,m-maleimidobenzoyl-N-hydroxysuccinimide ester (ICN Biochemicals, Inc.)or succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC,Pierce), all of which are hereby expressly incorporated by reference intheir entireties, is reacted with a NS3/4A protein or fragment thereofto form an activated molecule. That activated carrier is then reactedwith a polypeptide that either contains a terminal cysteine or to whichan additional amino- or carboxy-terminal cysteine residue has been addedto form a covalently bonded NS3/4A conjugate. As an alternative example,the amino group of a polypeptide hapten can be first reacted withN-succinimidyl 3-(2-pyridylthio)propionate (SPDP, Pharmacia), and thatthiol-containing polypeptide can be reacted with the activated NS3/4Aafter reduction. Of course, the sulfur-containing moiety and doublebond-containing Michael acceptor can be reversed. These reactions aredescribed in the supplier's literature, and also in Kitagawa, et al., J.Biochem., 79:233 (1976) and in Lachmann et al., in 1986 SyntheticPeptides as Antigens, (Ciba Foundation Symposium 119), pp. 25-40 (Wiley,Chichester: 1986), all of which are hereby expressly incorporated byreference in their entireties.

U.S. Pat. No. 4,767,842, herein expressly incorporated by reference inits entirety, teaches several modes of covalent attachment between acarrier and polypeptide that are useful here. In one method, tolylenediisocyanate is reacted with the NS3/4A or a fragment thereof in adioxane-buffer solvent at zero degrees C. to form an activated molecule.A polypeptide hapten (e.g., a T cell epitope) is thereafter admixed andreacted with the activated NS3/4A to form the covalently bonded NS3/4Aconjugate.

Particularly useful are a large number of heterobifunctional agents thatform a disulfide link at one functional group end and a peptide link atthe other, including N-succinimidyl-3-(2-pyridyldithio)propionate(SPDP). This reagent creates a disulfide linkage between itself and athiol in either the NS3/4A or fragment thereof or the hapten, forexample a cysteine residue in a polypeptide hapten, and an amide linkageon the coupling partner, for example the amino on a lysine or other freeamino group in the NS3/4A. A variety of such disulfide/amide formingagents are known. (See for example Immun. Rev. (1982) 62:185, hereinexpressly incorporated by reference in its entirety). Other bifunctionalcoupling agents form a thioether rather than a disulfide linkage. Manyof these thioether-forming agents are commercially available and includereactive esters of 6-maleimidocaproic acid, 2-bromoacetic acid,2-iodoacetic acid, 4-(N-maleimido-methyl)cyclohexane-1-carboxylic acidand the like. The carboxyl groups can be activated by combining themwith succinimide or 1-hydroxy-2-nitro-4-sulfonic acid, sodium salt. Theparticularly preferred coupling agent is succinimidyl4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) obtained fromPierce Company, Rockford, Ill. The foregoing list is not meant to beexhaustive, and modifications of the named compounds can clearly beused.

A polypeptide hapten (e.g., a T cell epitope) can be obtained in anumber of ways well known in the art. Usual peptide synthesis techniquescan be readily utilized. For example, recombinant and PCR-basedtechniques to produce longer peptides are useful. Because the desiredsequences are usually relatively short, solid phase chemical synthesisis useful.

As discussed below, DNA sequences that encode a variety of polypeptidehaptens (e.g., T cell epitopes) are known in the art. The codingsequence for peptides of the length contemplated herein can easily besynthesized by chemical techniques, for example, the phosphotriestermethod of Matteucci et al., J. Am. Chem. Soc. 103:3185 (1981). Ofcourse, by chemically synthesizing the coding sequence, any desiredmodification can be made simply by substituting the appropriate basesfor those encoding the native peptide sequence. The coding sequence canthen be provided with appropriate linkers and ligated into expressionvectors now commonly available in the art, and the regulating vectorsused to transform suitable hosts to produce the desired protein.

A number of such vectors and suitable host systems are now available.For example promoter sequences compatible with bacterial hosts areprovided in plasmids containing convenient restriction sites forinsertion of the desired coding sequence. Typical of such vectorplasmids are, for example, pUC8, and pUC13 available from J. Messing, atthe University of Minnesota (see, e.g., Messing et al., Nucleic AcidsRes. 9:309 (1981)) or pBR322, available from New England Biolabs.Suitable promoters include, for example, the beta-lactamase(penicillinase) and lactose (lac) promoter systems (Chang. et al.,Nature 198:1056 (1977) and the tryptophan (trp) promoter system (Goeddelet al., Nucleic Acids Res. 8:4057 (1980)). The resulting expressionvectors are transformed into suitable bacterial hosts using the calciumchloride method described by Cohen, et al., Proc. Natl. Acad. Sci.U.S.A. 69:2110 (1972). Successful transformants may produce the desiredpolypeptide fragments at higher levels than those found in strainsnormally producing the intact pili. Of course, yeast or mammalian cellhosts can also be used, employing suitable vectors and controlsequences.

Embodiments also include methods of using vaccine compositions andimmunogen preparations comprising the NS3/4A chimeric polypeptides orencoding nucleic acids, or a truncated or mutated version thereof, and,optionally, an adjuvant. The next section describes some of thesecompositions in greater detail.

Methods of Using the Vaccine Compositions and Immunogen Preparations

Routes of administration of the embodiments described herein include,but are not limited to, transdermal, parenteral, gastrointestinal,transbronchial, and transalveolar. Transdermal administration can beaccomplished by application of a cream, rinse, gel, etc. capable ofallowing the compositions described herein to penetrate the skin.Parenteral routes of administration include, but are not limited to,electrical or direct injection such as direct injection into a centralvenous line, intravenous, intramuscular, intraperitoneal, intradermal,or subcutaneous injection. Gastrointestinal routes of administrationinclude, but are not limited to, ingestion and rectal. Transbronchialand transalveolar routes of administration include, but are not limitedto, inhalation, either via the mouth or intranasally.

Compositions that are suitable for transdermal administration include,but are not limited to, pharmaceutically acceptable suspensions, oils,creams, and ointments applied directly to the skin or incorporated intoa protective carrier such as a transdermal device (“transdermal patch”).Examples of suitable creams, ointments, etc. can be found, for instance,in the Physician's Desk Reference. Examples of suitable transdermaldevices are described, for instance, in U.S. Pat. No. 4,818,540 issuedApr. 4, 1989 to Chinen, et al., hereby expressly incorporated byreference in its entirety.

Compositions that are suitable for parenteral administration include,but are not limited to, pharmaceutically acceptable sterile isotonicsolutions. Such solutions include, but are not limited to, saline,phosphate buffered saline and oil preparations for injection into acentral venous line, intravenous, intramuscular, intraperitoneal,intradermal, or subcutaneous injection.

Compositions that are suitable for transbronchial and transalveolaradministration include, but not limited to, various types of aerosolsfor inhalation. Devices suitable for transbronchial and transalveolaradministration of these are also embodiments. Such devices include, butare not limited to, atomizers and vaporizers. Many forms of currentlyavailable atomizers and vaporizers can be readily adapted to delivervaccines having ribavirin and an antigen.

Compositions that are suitable for gastrointestinal administrationinclude, but not limited to, pharmaceutically acceptable powders, pillsor liquids for ingestion and suppositories for rectal administration.

The nucleic acid constructs described herein, in particular, may beadministered by means including, but not limited to, traditionalsyringes, needleless injection devices, or “microprojectile bombardmentgene guns”. Alternatively, the genetic vaccine may be introduced byvarious means into cells that are removed from the individual. Suchmeans include, for example, ex vivo transfection, electroporation,microinjection and microprojectile bombardment. After the gene constructis taken up by the cells, they are reimplanted into the individual. Itis contemplated that otherwise non-immunogenic cells that have geneconstructs incorporated therein can be implanted into the individualeven if the vaccinated cells were originally taken from anotherindividual.

According to some embodiments, the gene construct is administered to anindividual using a needleless injection device. In other embodiments,the gene construct comprising the antigen of interest is provided to anindividual in need of an immune response to said antigen using anelectroporation device (e.g., a needle device or a needleless device).According to some embodiments, the gene construct is simultaneouslyadministered to an individual intradermally, subcutaneously andintramuscularly using a needleless injection device. Needlelessinjection devices, multi-needle electroporation devices, and nucleicacid electroporation devices, in general, are well known and widelyavailable (See e.g., U.S. Pat. No. 5,273,525, EP 1240917 B1, U.S. Pat.No. 5,702,359, EP 0874663B1,U.S. Pat. No. 6,418,341, U.S. Pat. No.6,763,264 U.S. Pat. No. 6,055,453, U.S. Pat. No. 6,233,482, U.S. Pat.No. 6,068,650, U.S. Pat. No. 6,014,584, U.S. Pat. No. 6,241,701, U.S.Pat. No. 6,516,223, U.S. Pat. No. 6,678,556, and U.S. Pat. No.6,110,161, hereby expressly incorporated by reference in theirentireties).

One having ordinary skill in the art can, following the teachingsherein, use needleless or needled electroporation devices (e.g.,providing the nucleic acid construct by hypodermic needle followed byelectroporation at the injection site) to deliver genetic material tocells of an individual. These gene construct delivery devices are wellsuited to deliver genetic material to all tissue. They are particularlyuseful to deliver genetic material to skin and muscle cells. In someembodiments, a needleless injection device may be used to propel aliquid or dissolvable substrate or carrier that comprises the nucleicacid construct (e.g., ballistic transformation) toward the surface ofthe individual's skin. The liquid is propelled at a sufficient velocitysuch that upon impact with the skin the liquid penetrates the surface ofthe skin, permeates the skin and muscle tissue therebeneath. Thus, thegenetic material is simultaneously administered intradermally,subcutaneously and intramuscularly. In some embodiments, a needlelessinjection device may be used to deliver genetic material to tissue ofother organs in order to introduce a nucleic acid molecule to cells ofthat organ.

Preferred embodiments include methods of enhancing an immune response toa desired antigen by providing an animal in need with an amount ofadjuvant (e.g., ribavirin) and one or more of the nucleic acid orpolypeptide compositions disclosed herein that is effective to enhancesaid immune response. In these embodiments, an animal in need of anenhanced immune response to an antigen/target is identified by usingcurrently available diagnostic testing or clinical evaluation. By oneapproach, for example, an individual infected with a virus, or afflictedwith cancer, is provided with the vaccine compositions described abovein an amount sufficient to elicit a cellular and humoral immune responseto a viral or cancer TCE so as to protect said individual from becominginfected with the virus, or to treat the cancer from which the TCE isderived. In another embodiment, an individual infected with a virus isidentified and provided with a vaccine composition comprising ribavirinand either a nucleic acid or polypeptide composition described herein,that includes a TCE from the virus and NS3/4A sequences in an amountsufficient to enhance the cellular and humoral immune response againstthe viral TCE so as to reduce or eliminate the viral infection.

The following Example describes the systematic mutation of residues inthe NS3 protease domain in order to elucidate the potential insertionsites for TCEs or TCEs and linkers, in which the chimeric NS3/4Aproteins retain protease activity.

Example 14

The serine protease cleavage domain of NS3/NS4A resides in the first 181amino acids of the peptide (Lin, C. et al., J. Virol., 68(12):8147-8157(1994)). FIG. 17 depicts the amino acid sequence of the proteasecleavage domain of the NS3/NS4A polypeptide from HCV isolate disclosedherein (SEQ ID NO: 39). To identify amino acid residues that affectprotease activity in the HCV isolate, mutations were made in each of the181 amino acids of the protease cleavage domain. Briefly, theNS3/NS4A-pVAX plasmid (described in Example 1) was used as a templatefor site-directed mutagenesis using the QUICKCHANGE™ mutagenesis kit(Stratagene), following the manufacturer's recommendations. Using thisapproach, NS3/NS4A-pVAX constructs encoding the polypeptides of (SEQ IDNO's: 40 through 220 and 1329-1339) were made. These constructs encodeNS3/NS4A polypeptides in which every residue other than alanine in (SEQID NO: 39) is changed to an alanine, and where every alanine in (SEQ IDNO: 39) is changed to a glycine. The resulting plasmids were sequencedto verify that the NS3/NS4A-pVAX vectors had been correctly made.Plasmids were grown in competent BL21 E. coli, and subsequently purifiedusing Qiagen DNA purification columns (Qiagen, Hamburg, Germany)according to the manufacturer's instructions. Purified plasmid DNA wasdissolved in phosphate buffered saline (PBS).

The resulting plasmids were transcribed and translated in vitro, and theresulting polypeptides were visualized by sodium dodecylsulfate-polyacrylamide gel electrophoresis (SDS-PAGE). In vitrotranscription and translation were performed using the T7 coupledreticulocyte lysate TNT™ system (Promega, Madison, Wis.) according tothe manufacturer's instructions. All in vitro translation reactions ofthe constructs were carried out at 30° C. with ³⁵S-labeled methionine(Amersham International, Plc, Buckinghamshire, UK). The labeled proteinswere separated by 12% SDS-PAGE and visualized by exposure to X-ray film(Hyper Film-MP, Amersham) for 6-18 hours.

When the assay described above is performed with wtNS3/NS4A-pVAX, theprotease activity of wtNS3/NS4A protein (SEQ ID NO: 2) is such that twoprotein bands are visualized on the autorad of the gel: a protein bandof approximately 67 kDa, which is consistent with the size of theNS3/NS4A uncleaved protein, and a protein band of approximately 61 kDa,which corresponds to the NS3 cleavage product from the reaction. Each ofthe 181 mutant NS3/NS4A-pVAX constructs was tested in the assaydescribed above. For each mutant construct assayed, the amount ofuncleaved (67 kDa) versus cleaved NS3/NS4A (61 kDa cleavage product) wascompared between the wtNS3/NS4A construct and the NS3/NS4A mutantconstruct, as a measure of how each mutation affected the proteaseactivity. As shown in Table 23, the following NS3/NS4A constructs haveamino acid substitutions that completely abolished protease activity:SEQ ID NOs: 87, 92, 96, 120, 124, 130, 136, 138, 162, 163, 178, 179,184, 192, 208, and 214. In reference to NS3 protease activity, the term“completely abolished” is meant to refer to polypeptides that have lessthan, equal to, or any number in between about 10%, 9%, 8%, 7%, 6%, 5%,4%, 3% 2% and 1% of the NS3 protease activity compared to the proteaseactivity of a wild type NS3 polypeptide or NS3/4A polypeptide (e.g., SEQID NO:36). In reference to NS3 protease activity, the term “reduced” ismeant to refer to polypeptides that have less than, equal to, or anynumber in between about 100%, 95%, 90%, 85%, 80%, 75%, 70%, 65%, 60%,55%, 50%, 45%, 40%, 35%, 30%, 25%, 20%, 15% and 10% of the NS3 proteaseactivity compared to the protease activity of a wild type NS3polypeptide or NS3/4A polypeptide (e.g., SEQ ID NO:36). The followingeight constructs have mutations that result in reduced proteaseactivity: SEQ ID NOs: 83, 133, 145, 147, 165, 182, 183, and 188.

As shown in Table 24, twenty two constructs have substitutions thatresult in enhanced (SEQ ID NOs: 45, 50, 52, 53, 69, 98, 103, 112, 115,125, 150, 161, 173, 175, 180, 200, 205, and 216), or greatly enhancedprotease activity (SEQ ID NOs: 91, 97, and 197). In reference to NS3protease activity, the term “enhanced” and “greatly enhanced” is meantto refer to polypeptides that have greater than, equal to, or any numberin between about 100%, 101%, 105%, 110%, 115%, 120%, 125%, 130%, 135%,140%, 145%, 150%, 155%, 160%, 165%, 170%, 175%, 180%, 185%, 190%, 195%,200%, 210%, 220%, 230%, 240%, 250%, 260%, 270%, 280%, 290%, 300%, 310%,320%, 330%, 340%, 350%, 360%, 370%, 380%, 390%, 400%, 425%, 450%, 475%,500%, 600% and 700% of the NS3 protease activity compared to theprotease activity of a wild type NS3 polypeptide or NS3/4A polypeptide(e.g., SEQ ID NO:36).

TABLE 23 Leu44Ala (SEQ ID NO: 83) Reduced Ile48Ala (SEQ ID NO: 87)Abolished Trp53Ala (SEQ ID NO: 92) Abolished His57Ala (SEQ ID NO: 96)Abolished Asp81Ala (SEQ ID NO: 120) Abolished Trp85Ala (SEQ ID NO: 124)Abolished Ala91Gly (SEQ ID NO: 130) Abolished Leu94Ala (SEQ ID NO: 133)Reduced Cys97Ala (SEQ ID NO: 136) Abolished Cys99Ala (SEQ ID NO: 138)Abolished Leu106Ala (SEQ ID NO: 145) Reduced Thr108Ala (SEQ ID NO: 147)Reduced Arg 123Ala (SEQ ID NO: 162) Abolished Gly124Ala (SEQ ID NO: 163)Abolished Leu126Ala (SEQ ID NO: 165) Reduced Ser139Ala (SEQ ID NO: 178)Abolished Gly140Ala (SEQ ID NO: 179) Abolished Leu143Ala (SEQ ID NO:182) Reduced Leu144Ala (SEQ ID NO: 183) Reduced Cys145Ala (SEQ ID NO:184) Abolished His149Ala (SEQ ID NO: 188) Reduced Ile153Ala (SEQ ID NO:192) Abolished Phe169Ala (SEQ ID NO: 208) Abolished Leu175Ala (SEQ IDNO: 214) Abolished

TABLE 24 Mutation Activity Tyr6Ala (SEQ ID NO: 45) Enhanced Arg11Ala(SEQ ID NO: 50) Enhanced Leu13Ala (SEQ ID NO: 52) Enhanced Leu14Ala (SEDID NO: 53) Enhanced Glu30Ala (SEQ ID NO: 69) Enhanced Cys52Ala (SEQ IDNO: 91) Greatly enhanced Gly58Ala (SEQ ID NO: 97) Greatly enhancedAla59Gly (SEQ ID NO: 98) Enhanced Ile64Ala (SEQ ID NO: 103) EnhancedGln73Ala (SEQ ID NO: 112) Enhanced Thr76Ala (SEQ ID NO: 115) EnhancedPro86Ala (SEQ ID NO: 125) Enhanced Ala111Gly (SEQ ID NO: 150) EnhancedGly 122Ala (SEQ ID NO: 161) Enhanced Tyr 134Ala (SEQ ID NO: 173)Enhanced Lys 136Ala (SEQ ID NO: 175) Enhanced Gly 141Ala (SEQ ID NO:180) Enhanced Val158Ala (SEQ ID NO: 197) Greatly Enhanced Arg161Ala (SEQID NO: 200) Enhanced Ala166Gly (SEQ ID NO: 205) Enhanced Thr177Ala (SEQID NO: 216) Enhanced

Protease activity is associated with viral assembly and maturation (See,e.g., Babé et al., Cell, 91:427-430 (1997)). Accordingly, mutantNS3/NS4A polypeptides with altered protease activity and their encodingnucleic acids are useful in the immunogenic compositions describedherein. The fragments listed in TABLES 23-24 are preferred immunogensthat can be incorporated with or without an adjuvant (e.g., ribavirin)into a composition for administration to an animal so as to induce animmune response in said animal to HCV.

As shown in TABLE 25, the following NS3/4A constructs have amino acidsubstitutions that did not have a large effect (SEQ ID NOs: 40, 48-49,54, 56, 60-61, 66, 72, 74-75, 77-79, 82, 85, 89, 100-102, 107-110,113-114, 121, 131, 144, 146, 148-149, 152-153, 156, 160, 166, 167,170-171, 177, 181, 185-186, 189-190, 194-195, 198-199, 204, 206, 209,210, 213, 215, and 217), or did not have any detectable effect onprotease activity (SEQ ID NOs: 41-44, 46, 47, 51, 55, 58, 59, 62, 65,67-68, 70-71, 73, 76, 80-81, 84, 86, 88, 90, 93, 95, 99, 104-106, 111,116-119, 123, 127-129, 134-135, 137, 139-143, 151, 154-155, 157-159,164, 168-169, 172, 176, 191, 193, 196, 201-203, 211-212, and 218-220).The fragments listed in TABLE 22 are preferred immunogens that can beincorporated with or without an adjuvant (e.g., ribavirin) into acomposition for administration to an animal so as to induce an immuneresponse in said animal to HCV.

TABLE 25 Mutation Activity Ala1Gly (SEQ ID NO: 40) Little Effect Pro2Ala(SEQ ID NO: 41) No Effect Ile3Ala (SEQ ID NO: 42) No Effect Thr4Ala (SEDID NO: 43) No Effect Ala5Gly (SEQ ID NO: 44) No Effect Ala7Gly (SEQ IDNO: 46) No Effect Gln8Ala (SEQ ID NO: 47) No Effect Gln9Ala (SEQ ID NO:48) Little Effect Thr10Ala (SEQ ID NO: 49) Little Effect Gly12Ala (SEQID NO: 51) No Effect Gly15Ala (SEQ ID NO: 54) Little Effect Cys16Ala(SEQ ID NO: 55) No Effect Ile17Ala (SEQ ID NO: 56) Little EffectThr19Ala (SEQ ID NO: 58) No Effect Ser20Ala (SEQ ID NO: 59) No EffectLeu21Ala (SEQ ID NO: 60) Little Effect Thr22Ala (SEQ ID NO: 61) LittleEffect Gly23Ala (SEQ ID NO: 62) No Effect Lys26Ala (SEQ ID NO: 65) NoEffect Asn27Ala (SEQ ID NO: 66) Little Effect Gln28Ala (SEQ ID NO: 67)No Effect Val29Ala (SEQ ID NO: 68) No Effect Gly31Ala (SEQ ID NO: 70) NoEffect Glu32Ala (SEQ ID NO: 71) No Effect Val33Gly (SEQ ID NO: 72)Little Effect Gln34Ala (SEQ ID NO: 73) No Effect Ile35Ala (SEQ ID NO:74) Little Effect Val36Ala (SEQ ID NO: 75) No Effect Ser37Ala (SEQ IDNO: 76) Little Effect Thr38Ala (SEQ ID NO: 77) Little Effect Ala39Gly(SEQ ID NO: 78) Little Effect Ala40Gly (SEQ ID NO: 79) Little EffectGln41Ala (SEQ ID NO: 80) No Effect Thr42Ala (SEQ ID NO: 81) No EffectPhe43Ala (SEQ ID NO: 82) Little Effect Ala45Gly (SEQ ID NO: 84) NoEffect Thr46Ala (SEQ ID NO: 85) Little Effect Cys47Ala (SEQ ID NO: 86)No Effect Gln49Ala (SEQ ID NO: 88) No Effect Gly50Ala (SEQ ID NO: 89)Little Effect Val51Ala (SEQ ID NO: 90) Little Effect Thr54Ala (SEQ IDNO: 93) No Effect Arg161Ala (SEQ ID NO: 95) No Effect Ala56Gly (SEQ IDNO: 99) No Effect Phe57Ala (SEQ ID NO: 100) Little Effect Leu58Ala (SEQID NO: 101) No Effect Thr63Ala (SEQ ID NO: 102) Little Effect Thr64Ala(SEQ ID NO: 103) No Effect Ala65Gly (SEQ ID NO: 104) No Effect Ser66Ala(SEQ ID NO: 105) No Effect Pro67Ala (SEQ ID NO: 106) No Effect Lys68Ala(SEQ ID NO: 107) Little Effect Gly69Ala (SEQ ID NO: 108) Little EffectPro70Ala (SEQ ID NO: 109) Little Effect Val71Ala (SEQ ID NO: 110) LittleEffect Ile72Ala (SEQ ID NO: 111) Little Effect Met74Ala (SEQ ID NO: 113)Little Effect Tyr75Ala (SEQ ID NO: 114) Little Effect Gln77Ala (SEQ IDNO: 116) No Effect Val78Ala (SEQ ID NO: 117) No Effect Asp79Ala (SEQ IDNO: 118) No Effect Gln80Ala (SEQ ID NO: 119) No Effect Leu82Ala (SEQ IDNO: 121) Little Effect Gly84Ala (SEQ ID NO: 123) No Effect Pro88Ala (SEQID NO: 127) No Effect Gln89Ala (SEQ ID NO: 128) No Effect Gly90Ala (SEQID NO: 129) No Effect Arg92Ala (SEQ ID NO: 131) Little Effect Thr95Ala(SEQ ID NO: 134) No Effect Pro96Ala (SEQ ID NO: 135) No Effect Thr98Ala(SEQ ID NO: 137) No Effect Gly100Ala (SEQ ID NO: 139) No EffectSer101Ala (SEQ ID NO: 140) No Effect Ser102Ala (SEQ ID NO: 141) NoEffect Asp103Ala (SEQ ID NO: 142) No Effect Leu104Ala (SEQ ID NO: 143)No Effect Try105Ala (SEQ ID NO: 144) Little Effect Val107Ala (SEQ ID NO:146) Little Effect Arg109Ala (SEQ ID NO: 148) Little Effect His110Ala(SEQ ID NO: 149) Little Effect Asp112Ala (SEQ ID NO: 151) No EffectVal113Ala (SEQ ID NO: 152) Little Effect Ile114Ala (SEQ ID NO: 153)Little Effect Pro115Ala (SEQ ID NO: 154) No Effect Val116Ala (SEQ ID NO:155) No Effect Arg118Ala (SEQ ID NO: 157) No Effect Arg119Ala (SEQ IDNO: 158) Little Effect Gly120Ala (SEQ ID NO: 159) No Effect Asp121Ala(SEQ ID NO: 160) Little Effect Ser125Ala (SEQ ID NO: 164) No EffectLeu127Ala (SEQ ID NO: 166) Little Effect Ser128Ala (SEQ ID NO: 167)Little Effect Pro129Ala (SEQ ID NO: 168) No Effect Arg130Ala (SEQ ID NO:169) No Effect Pro131Ala (SEQ ID NO: 170) Little Effect Ile132Ala (SEQID NO: 171) Little Effect Ser133Ala (SEQ ID NO: 172) No Effect Gly137Ala(SEQ ID NO: 176) No Effect Ser138Ala (SEQ ID NO: 177) Little EffectPro142Ala (SEQ ID NO: 181) Little Effect Pro146Ala (SEQ ID NO: 185)Little Effect Ala147Gly (SEQ ID NO: 186) Little Effect Ala150Gly (SEQ IDNO: 189) Little Effect Val151Gly (SEQ ID NO: 190) Little EffectGly152Ala (SEQ ID NO: 191) No Effect Phe154Ala (SEQ ID NO: 193) NoEffect Arg155Ala (SEQ ID NO: 194) Little Effect Ala156Gly (SEQ ID NO:195) Little Effect Ala157Gly (SEQ ID NO: 196) No Effect Cys159Ala (SEQID NO: 198) Little Effect Thr160Ala (SEQ ID NO: 199) Little EffectGly162Ala (SEQ ID NO: 201) No Effect Val163Ala (SEQ ID NO: 202) NoEffect Ala164Gly (SEQ ID NO: 203) No Effect Lys165Ala (SEQ ID NO: 204)Little Effect Val167Ala (SEQ ID NO: 206) Little Effect Ile170Ala (SEQ IDNO: 209) Little Effect Pro171Ala (SEQ ID NO: 210) Little EffectVal172Ala (SEQ ID NO: 211) No Effect Glu173Ala (SEQ ID NO: 212) NoEffect Ser174Ala (SEQ ID NO: 213) Little Effect Glu176Ala (SEQ ID NO:215) Little Effect Thr178Ala (SEQ ID NO: 217) Little Effect Met179Ala(SEQ ID NO: 218) No Effect Arg180Ala (SEQ ID NO: 219) No EffectSer181Ala (SEQ ID NO: 220) No Effect

The mutant HCV genes and the encoded polypeptides disclosed herein areuseful as novel research tools for drug discovery. Specifically,polypeptides exhibiting enhanced protease activity can be used in assaysto identify novel compounds that inhibit protease activity. Suchscreening assays will include assays amenable to high-throughputscreening of chemical libraries, making them particularly suitable foridentifying small molecule drug candidates. Small molecules contemplatedinclude synthetic organic or inorganic compounds. The assays can beperformed in a variety of formats, including protein-protein bindingassays, biochemical screening assays, immunoassays and cell basedassays, which are well characterized in the art.

The HCV genes encoding polypeptides with altered protease activity areuseful in the creation of transgenic organisms, as described herein inparagraphs [0183]-[0184]. Transgenic organisms expressing mutant HCVpolypeptides are useful as model organisms for the study of HCVreplication and life cycle.

Example 15

Two particular mutants, Val1055Ala (corresponding to Val29Ala of SEQ IDNO: 68) and Gln1060Ala (corresponding to Gln34Ala of SEQ ID NO: 73),were tested for their ability to proteolytically cleave the NS3-NS4Ajunction while not cleaving the human IPS-1 molecule to ΔIPS-1. Asdetailed in above, Val29Ala of SEQ ID NO: 68 and Gln34Ala of SEQ ID NO:73 were tested for their ability to affect the protease activity in theHCV isolate. These mutants were found through mutagenesis of the NS3protease domain wherein the residues depicted in FIG. 18 were replacedwith Alanine or Glycine and tested for their effect on cleavage of theNS3-NS4A cleavage site (also depicted in FIG. 18). Also mentioned above,these two mutants did not have a large effect on protease activity inthe HCV isolate. These mutants were further tested for their ability tocleave the human IPS-1 molecule to ΔIPS-1.

Cells were cotransfected with a plasmid coding for the human IPS-1 geneas well as a pVAX1 plasmid expressing the mutant NS3/4A gene. 36 hourslater the cells were lyse. Cleaved and uncleaved IPS-1 peptides werevisualized on an SDS-PAGE gel after a Western blot with antibodiesspecific for the IPS-1 fragments. As shown in FIGS. 19A and 19BVal1055Ala (corresponding to Val29Ala of SEQ ID NO: 68) and Gln1060Ala(corresponding to Gln34Ala of SEQ ID NO: 73) were not able to cleaveIPS-1 to ΔIPS-1.

Example 16

A particular mutant, containing two amino acid mutations Val1055Ala andGln1060Ala (corresponding to Val29Ala and Gln34Ala, respectively, of SEQID NO: 1329), is created by combining the mutations present in SEQ IDNOs.: 68 and 73. The residues referred to as 1055 and 1060 vary by 1026amino acids from the listed sequences as the NS3/4A gene begins atresidue 1026 of the HCV polyprotein. This mutant is tested for itsaffect on the proteolytic cleavage of the NS3-NS4A junction as inExample 15. Results show that the mutant does not have a large effect onprotease activity in the HCV isolate.

This mutant is further tested for its ability to cleave the human IPS-1molecule to ΔIPS-1 as detailed above. Results show that the IPS-1 geneis not cleaved to ΔIPS-1 by the mutant represented by SEQ ID NO: 1329.

Example 17

NS3 protease mutants represented by SEQ ID NOs: 1330-1339 are tested fortheir ability to affect NS3 protease cleavage at the NS3-NS4A proteasecleavage site, as explained in above. Mutants having no effect, littleeffect, no substantial effect, or heightened effect on protease cleavageat the NS3-NS4A protease cleavage site are selected for further testing.

These mutants are further tested for their ability to cleave the humanIPS-1 molecule to ΔIPS-1 as detailed above. Mutants that cannot cleaveIPS-1 to ΔIPS-1 are selected as favorable mutants.

Example 18

Mutants containing two or more amino acid mutations, created bycombining any number of favorable mutants described above, are created.These mutants are tested for their ability to affect NS3 proteasecleavage at the NS3-NS4A protease cleavage site, as detailed in above.Mutants having no effect, little effect, no substantial effect, orheightened effect on protease cleavage at the NS3-NS4A protease cleavagesite are selected for further testing.

These mutants are further tested for their ability to cleave the humanIPS-1 molecule to ΔIPS-1 as detailed above. Mutants that cannot cleaveIPS-1 to ΔIPS-1 are selected as favorable mutants.

Although the invention has been described with reference to embodimentsand examples, it should be understood that various modifications can bemade without departing from the spirit of the invention. Accordingly,the invention is limited only by the following claims.

The next example demonstrates that chimeric NS3/4A nucleic acids andencoded polypeptides described herein prime CTL responses to the T cellepitopes encoded therein.

Example 19

The Hepatitis B viral core protein (HBc) has been disclosed as animmunogenic moiety that stimulates the T cell response of an immunizedhost animal. See, e.g, U.S. Pat. No. 4,818,527, U.S. Pat. No. 4,882,145and U.S. Pat. No. 5,143,726. More particularly, the sequence of SEQ IDNO:1014 of the Hepatitis B core protein has been shown to elicit aspecific T-cell response when administered to mice. To assess theability of SEQ ID NO:1014 DNA constructs to prime CTLs, the nucleic acidof SEQ ID NO:1015 is cloned into the pVAX1 expression vector(Invitrogen, Carlsbad, Calif.) to create HBcAg-pVAX1.

Plasmids are grown in BL21 E. coli cells, and sequenced for accuracy.Plasmid DNA used for in vivo vaccination is purified using Qiagen DNApurification columns, according to the manufacturer's instructions(Qiagen GmbH, Hilden, FRG). The concentration of the resulting plasmidDNA is determined spectrophotometrically (Dynaquant, Pharmacia Biotech,Uppsala, Sweden) and the purified DNA is dissolved in sterile phosphatebuffered saline (PBS) at a concentration of 1 mg/ml.

Groups of eight to ten C57/BL6 mice are primed with HBcAg-pVAX1 intramuscularly (i.m.) or using a gene gun. For i.m. delivery, mice areimmunized by needle injections of 100 μg plasmid DNA givenintramuscularly to the tibialis anterior (TA) muscle. 5 days prior toDNA immunization, mice are injected intramuscularly with 50 μl per TAmuscle of 0.01 mM cardiotoxin (Latoxan) in 0/9% sterile saline. The miceare boosted with a second injection of 100 μg plasmid DNA four weekssubsequent to the first DNA immunization. For gene gun delivery, plasmidDNA is linked to gold particles according to protocols supplied by themanufacturer (Bio-Rad Laboratories, Hercules, Calif.). Prior toimmunization, the injection area is shaved and the immunization isperformed according to the manufacturer's protocol. Each injection dosecontains 4 μg of plasmid DNA. Immunizations are performed on weeks 0 and4.

The presence of CTLs specific for SEQ ID NO:1014 is assayed using astandard ⁵¹Cr-release assay. Briefly, spleen cells are harvested frommice 14 days after the initial immunization or the booster immunization.Chromium release assays are performed as described in Lazdina, et al.(2003) J. Gen. Virol. 84:1-8, herein expressly incorporated by referencein its entirety. Single cell suspensions are prepared. 25×10⁶splenocytes are restimulated with 25×10⁶ syngenic irradiated (20 Gy)splenocytes pulsed with 0.05 μM peptide, as previously described.Sandberg et al. (2000) J. Immunol. 165:25-33, herein expresslyincorporated by reference in its entirety. Restimulation cultures areset in 12 ml complete RPMI medium (Gibco). After 5 days, effector cellsare harvested and washed twice. RMA-S target cells (Karre et al. (1986)Nature 319:675-678) are pulsed with 50 μM peptide for 90 min at 5% CO₂and 37° C. Serial dilutions of effector cells are incubated with 5×103chromium-labeled peptide pulsed RMA-S target cells in a final volume of200 μl per well in 96-well plates. After a 4 hour incubation at 5% CO₂and 37° C., 100 μl of supernatant is collected and the radioactivity isdetermined using a γ counter. The percentage of specific release iscalculated according to the formula: (Experimental release−spontaneousrelease/total release−spontaneous release)×100.

The results of the ⁵¹Cr-release assay is shown in FIG. 20A. i.m.injection of HBcAg-pVAX1 elicits a cellular immune response. Bycontrast, immunization with HBcAg-pVAX1 via a gene gun does not elicit acellular immune response. FIG. 20B.

In another set of experiments, the presence of CTLs specific for the SEQID NO:1014 is assayed using a standard ELISPOT assay to detectγ-IFN-secreting CTLs. Current Protocols in Immunology, Edited by: JohnE. Coligan, Ada M. Kruisbeek, David H. Margulies, Ethan M. Shevach,Warren Strober (2001 John Wiley & Sons, NY, N.Y.)

In still another set of experiments, the NS3/4A chimeric polypeptidesencoded by the nucleic acids are used to immunize mice, using standardimmunization procedures for polypeptides such as those disclosed inco-pending U.S. Patent Application No. 60/685,014, the contents of whichis hereby expressly incorporated by reference in its entirety.

In contrast to HBcAg-pVAX1, nucleic acids encoding the NS3/4A peptidecan effectively prime CTLs by both intra muscular and gene gun delivery.See, e.g., co-pending U.S. Provisional Patent Application No.60/685,014. To demonstrate that NS3/4A functions as a T-cell epitopecarrier, chimeric NS3/4A nucleic acids that include the TCE encoded bySEQ ID NO:1015, or the encoded polypeptides, are tested for theirability to prime CTLs by both i.m. and gene gun delivery. TheNS3/4A-pVAX vector described in Example 1 is used to generate NS3/4Achimeric expression vectors containing in-frame fusions of SEQ IDNO:1015 using standard cloning techniques. See, Ausubel et al., supra.The chimeric NS3/4A expression vectors contain in-frame fusions of SEQID NO:1015 to the 5′ end of the NS3/4A coding sequence; to the 3′ end ofthe NS3/4A coding sequence, and within the NS3/4A coding sequence suchthat the epitope of SEQ ID NO:1015 is between amino acids 181 and 182 ofSEQ ID NO: 36, between amino acid residues 453 and 513 of SEQ ID NO:36(e.g., SEQ ID NO:1013, which encodes the NS3/4A chimeric polypeptide ofSEQ ID NO:1012) or in analogous positions in any NS3/4A polypeptide, orelsewhere within the NS3/4A polypeptide. The chimeric NS3/4A nucleicacids are delivered to mice either intramuscularly or using a gene gun,as described herein. Specific CTL responses are measured using a⁵¹Cr-release assay or ELIspot assay.

The ability of the chimeric NS3/4A vectors to prime CTLs is similarwhether the vector is administered intramuscularly or using a gene gun,demonstrating that presentation of epitopes in the context of NS3/4Aeffectively primes CTLs against the epitopes. This example also suggeststhat the NS3/4A platform is useful for generating immune responses toHBV TCEs that elicit immune responses in humans, (e.g., SEQ ID SEQ IDNO:351).

The following example describes the generation and validation ofimmunogenic compositions that generate or enhance CTL priming tospecific antigens.

Example 20

Chimeric NS3/4A nucleic acid constructs encoding at least one TCEjuxtaposed to or inserted within various positions along the NS3/4Apolypeptide are made and assayed for their ability to prime an immuneresponse to the TCE. Chimeric polypeptides encoded by the NS3/4Achimeric nucleic acids are also assayed for their ability to prime animmune response to the encoded TCE. A TCE to which a CTL response isdesired (e.g., any one of the TCEs presented herein, including SEQ IDNOs: 221-271, SEQ ID NOs:809-1011, and SEQ ID NO:1014) is selected.Using standard cloning techniques, the nucleic acid encoding the TCE(e.g., any one of the TCEs presented herein, including SEQ ID NOs:221-271, SEQ ID NOs:809-1011, and SEQ ID NO:1014) is cloned into theNS3/4A-pVAX vector described in Example 1, or an equivalent thereof(e.g., an NS3/4A-pVAX vector wherein the NS3/4A sequence is selectedfrom the group of SEQ ID NOs: 572-808) to generate a chimericNS3/4A-pVAX vector. The chimeric NS3/4A-pVAX vectors encode chimericNS3/4A polypeptides in which the TCE is juxtaposed to the N-terminus orC-terminus of the NS3/4A polypeptide, or is located within the NS3/4Apolypeptide (e.g., between amino acids 181 and 182 of SEQ ID NO: 2).

Plasmids that have been sequenced for accuracy are purified and preparedfor use in immunization as described in Example 19. Alternatively,polypeptides encoded by said nucleic acids are expressed and used inimmunizations as described in Example 19. Mice are primed with thechimeric NS3/4A-pVAX nucleic acids intra muscularly (i.m.) or using agene gun as described in Example 19, or by another method (e.g., usingelectroporation (Innovio, Oslo, Sweden) according to the manufacturer'sinstructions).

The priming of CTLs specific for the TCE (e.g., an epitope listed inpresented herein, including SEQ ID NOs: 221-271, SEQ ID NOs:809-1011,and SEQ ID NO:1014) is assayed using a standard ⁵¹Cr-release assay or astandard ELISPOT assay to detect γ-IFN-secreting CTLs. Data from the⁵¹Cr-release assay or the ELISPOT assay are used to determine preferredsites of insertion of the TCE within the NS3/4A-pVAX vector

Chimeric NS3/4A expression vectors contain in-frame fusions of TCEs(e.g., an epitope listed in presented herein, including SEQ ID NOs:221-271, SEQ ID NOs:809-1011, and SEQ ID NO:1014) to the 5′ end of theNS3/4A coding sequence; to the 3′ end of the NS3/4A coding sequence, andwithin the NS3/4A coding sequence such that the TCE is between aminoacids 181 and 182 of SEQ ID NO: 36, between amino acid residues 453 and513 of SEQ ID NO:36, or in analogous positions in any NS3/4Apolypeptide, or elsewhere within the NS3/4A polypeptide. The chimericNS3/4A nucleic acids or encoded polypeptides are delivered to miceeither intramuscularly or using a gene gun, as described herein.Specific CTL responses are measured using a ⁵¹Cr-release assay orELISPOT assay as described in Example 3.

For each TCE, preferred sites of insertion within an NS3/4A nucleicacid, or juxtaposed to the NS3/4A nucleic acid are determined bycomparing the immune responses generated by the chimeric nucleic acidsor encoded polypeptides. Accordingly, provided herein are methods ofmaking an immunogen that can include the steps of a) identifying a TCEagainst which an immune response is desired b) generating at least onechimeric NS3/4A nucleic acid in which the DNA sequence encoding the TCEis juxtaposed to or inserted within the NS3/4A sequence (e.g., SEQ IDNO: 1), and c) detecting the immune response generated by the chimericNS3/4A nucleic acid or encoded polypeptide.

Example 21

The Hepatitis B viral core protein (HBc) is an immunogen that stimulatesthe T cell response of an immunized host animal. See, e.g, U.S. Pat. No.4,818,527, U.S. Pat. No. 4,882,145 and U.S. Pat. No. 5,143,726, all ofwhich are hereby expressly incorporated by reference in theirentireties. In fact, the Hepatitis B core protein (HBcAg) has been shownto elicit a specific T-cell response in immunized mice. It iscontemplated that DNA immunogens that are codon-optimized for expressionin humans and which encode the HCV NS3/4A platform and fragments ofHBcAg separated by NS3 protease cleavage sites will effectively primeHBcAg-specific CTLs, stimulate HBcAg-specific proliferative T cellresponses, and induce production of HBcAg-specific antibodies in animalswhen these DNA immunogens are delivered by various DNA vaccinationmethodologies. In some embodiments, it is contemplated that the DNAimmunogens, which are codon-optimized for expression in humans and whichencode the HCV NS3/4A platform and fragments of HBcAg separated by NS3protease cleavage sites will be more effective at priming HBcAg-specificCTLs, stimulating HBcAg-specific proliferative T cell responses, andinducing production of HBcAg-specific antibodies in animals thanconventional DNA immunogens that encode HBcAg antigens and moreeffective than DNA immunogens that encode the NS3/4A platform andfragments of HBcAg without NS3 protease cleavage sites.

To determine the immunogenicity of codon-optimized DNA constructsencoding the HCV NS3/4A platform and fragments of HBcAg separated by NS3protease cleavage sites and to compare the efficiency of theseconstructs with conventional HBcAg-containing constructs with andwithout the NS3/4A platform, several codon-optimized DNA constructsencoding the HCV NS3/4A platform and fragments of HBcAg separated by NS3protease cleavage sites including antigenic sequences in variousorientations are made (see SEQ ID NOs: 1174-1198 and FIG. 1).Codon-optimized DNA constructs encoding only the HBcAg and/or fragmentsthereof or encoding the NS3/4A platform and the HBcAg and/or fragmentsthereof without NS3 protease cleavage sites are also made forcomparison. Codon optimized DNA encoding the HCV NS3/4A platform andfragments of HBcAg in various orientations separated by NS3 proteasecleavage sites are cloned into the pVAX1 expression vector (Invitrogen,Carlsbad, Calif.) or other suitable DNA vaccination vectors. Once theconstructs are made, they are provided to animals by a DNA vaccinationmethodology (e.g., injection, electroporation, such as MedPulser®, orintranasal or transdermal delivery). Analysis of the presence and amountof HBcAg-specific CTLs can then be made before during and after severalintroductions of the constructs (e.g., an initial introduction followedby one, two, three, four, or five boosting events). It will be shownthat the presence of the HCV NS3/4A platform provides a more robust DNAimmunogen, as compared to immunogens that lack the NS3/4A platform, andthat the presence of one or more NS3/4A protease cleavage sites withinthe antigen also improves immunogenicity. It is also expected that thepresence of shuffled HBcAg antigenic fragments (e.g., SEQ ID NOs:1191-1198) within the antigen will provide a greater immune responsethan the unshuffled native antigen or fragments thereof. The followingdescribes these experiments in greater detail.

Plasmids containing the codon-optimized (human) DNA immunogens encodingthe HCV NS3/4A platform and fragments of HBcAg separated by the NS3/4Aprotease cleavage site will be grown in BL21 E. coli cells, andsequenced for accuracy. Although the fragments of HBcAg are separated bythe NS3/4A protease cleavage site, any NS3 protease cleavage site can beused (e.g., NS4A/B, NS4B/5A, and NS5A/B). The NS3/4A platform isseparated from the fragments of HBcAg by an NS4A/B cleavage site,although any NS3 protease cleavage site can be used. In the construct,the NS3 platform is separated from the NS4A by the NS3/4A proteasecleavage site, although any NS3 protease cleavage site can be used.Plasmids containing the conventional HBcAg sequence and/or fragmentsthereof will also be grown for comparison. Plasmid DNA used for in vivovaccination is then purified using Qiagen DNA purification columns,according to the manufacturer's instructions (Qiagen GmbH, Hilden, FRG).The concentration of the resulting plasmid DNA is determinedspectrophotometrically (Dynaquant, Pharmacia Biotech, Uppsala, Sweden)and the purified DNA is dissolved in sterile phosphate buffered saline(PBS) at a concentration of approximately 1 mg/ml.

Groups of eight to ten C57/BL6 mice or New Zealand rabbits are primedwith an HBcAg-containing construct (see SEQ ID NOs: 1174-1198 andFIG. 1) intranasally, transdermally, intra muscularly (i.m.), or usingan electroporation device (e.g., MedPulser®).

If a transdermal or intranasal delivery is evaluated, an amount ofplasmid DNA that is sufficient to deliver approximately 70 μg-100 μg ofplasmid DNA per dose is formulated with the delivery vehicle. Animalsare then provided the plasmid DNA one, two, three, four, or five timesat monthly intervals. Prior to transdermal immunization, the deliveryarea is shaved.

If intramuscular injection is evaluated, animals are immunized i.m withapproximately 70-100 μg plasmid DNA at the tibialis anterior (TA)muscle. 5 days prior to DNA immunization, animals may also be injectedintramuscularly with 50 μl per TA muscle of 0.01 mM cardiotoxin(Latoxan) in 0/9% sterile saline.

When electroporation is evaluated, animals are immunized i.m withapproximately 70-100 μg plasmid DNA at the tibialis anterior (TA) muscleand immediately after injection, the Medpulser® is applied with a 0.5 cmneedle array set to deliver two 60 ms pulses of 246 V/cm to theinjection site. In mice, one two needle electrode tip is used and whenrabbits are used, one four needle electrode tip is used per injectionper animal. The procedure can be repeated up to three times in mice andup to five times in rabbits at monthly intervals.

If gene gun delivery is performed, plasmid DNA is linked to goldparticles according to protocols supplied by the manufacturer (Bio-RadLaboratories, Hercules, Calif.). Prior to immunization, the injectionarea is shaved and the immunization is performed according to themanufacturer's protocol. Each injection dose by gene gun contains 4-100μg of plasmid DNA. Immunizations are performed on weeks 0 and 4.

The presence of CTLs specific for HBcAg is then assayed using a standard⁵¹Cr-release assay. Briefly, spleen cells are harvested from immunizedanimals 14 days after the initial immunization or a boosterimmunization. Chromium release assays are performed as described inLazdina, et al. (2003) J. Gen. Virol. 84:1-8, herein expresslyincorporated by reference in its entirety. Single cell suspensions areprepared. 25×10⁶ splenocytes are restimulated with 25×10⁶ syngenicirradiated (20 Gy) splenocytes pulsed with 0.05 μM peptide, aspreviously described. Sandberg et al. (2000) J. Immunol. 165:25-33,herein expressly incorporated by reference in its entirety.Restimulation cultures are set in 12 ml complete RPMI medium (Gibco).After 5 days, effector cells are harvested and washed twice. RMA-Starget cells (Karre et al. (1986) Nature 319:675-678) are pulsed with 50μM peptide for 90 min at 5% CO₂ and 37° C. Serial dilutions of effectorcells are incubated with 5×10³ chromium-labeled peptide pulsed RMA-Starget cells in a final volume of 200 μl per well in 96-well plates.After a 4 hour incubation at 5% CO₂ and 37° C., 100 μl of supernatant iscollected and the radioactivity is determined using a γ counter. Thepercentage of specific release is calculated according to the formula:(Experimental release−spontaneous release/total release−spontaneousrelease)×100. The results of the ⁵¹Cr-release assay will show that thepresence of the HCV NS3/4A platform provides a more robust DNAimmunogen, as compared to immunogens that lack the NS3/4A platform, andthat the presence of one or more NS3/4A protease cleavage sites withinthe antigen also improves immunogenicity. The assay will further showthat the presence of shuffled HBcAg antigenic fragments (e.g., SEQ IDNOs: 1191-1198) within the antigen will provide a greater immuneresponse than the unshuffled native antigen or fragments thereof.

In another set of experiments, the presence of γ-IFN-secreting CTLs andT helper (Th) cells to HBcAg in splenocyte or lymph node cultures willbe evaluated using a commercially available ELISpot assay. (See CurrentProtocols in Immunology, Edited by: John E. Coligan, Ada M. Kruisbeek,David H. Margulies, Ethan M. Shevach, Warren Strober (2001 John Wiley &Sons, NY, N.Y.), herein expressly incorporated by reference in itsentirety). By this approach, the number of γ-IFN-secreting CTLs or spotsis determined at various concentrations of peptide. These experimentswill show that the presence of the HCV NS3/4A platform provides a morerobust DNA immunogen, as compared to immunogens that lack the NS3/4Aplatform, and that the presence of one or more NS3/4A protease cleavagesites within the antigen also improves immunogenicity. The assay willfurther show that the presence of shuffled HBcAg antigenic fragments(e.g., SEQ ID NOs: 1191-1198) within the antigen will provide a greaterimmune response than the unshuffled native antigen or fragments thereof.

In still another set of experiments, the proliferative responses toHbcAg in whole blood obtained from immunized animals is determined. Anamount of whole blood is obtained from the animal (e.g., approximately 4ml from a rabbit), prior to the first vaccination and two weeks aftereach vaccination. The blood is collected in Heparin tubes and the plasmaand peripheral mononuclear cells (PBMCs) are isolated by gradientcentrifugation. The plasma is stored at −80 degrees Centrigrade untilanalysis for HBcAg-specific antibodies. The presence and amount ofantibodies specific for HBcAg in the various samples can be measuredusing an ELISA assay. The PBMCs are immediately assayed for in vitroproliferative recall responses using a standard 96 h proliferationassay. (See Lazinda et al., J. Gen. Virol. 82:1299-1308 (2001), hereinexpressly incorporated by reference in its entirety.) In brief,microtiter plates are seeded with approximately 200,000 cells/well andthe cells are incubated with media alone, phytohemagglutinin (PHA) orrecombinant HbcAg. After 72 hours, radioactive thymidine is added and16-24 hours later the cells are harvested, The proliferation isdetermined as radioactivity of the cells as the counts per minute (cpm)of cells incubated with the antigen divided by the CPM of the cellsincubated with the media alone (sample to negative ration; S/N). Groupsare compared by the mean S/N ratios at several time points). Theseexperiments will show that the presence of the HCV NS3/4A platformprovides a more robust DNA immunogen, as compared to immunogens thatlack the NS3/4A platform, and that the presence of one or more NS3/4Aprotease cleavage sites within the antigen also improves immunogenicity.The assay will also show that the presence of shuffled HBcAg antigenicfragments (e.g., SEQ ID NOs: 1191-1198) within the antigen will providea greater immune response than the unshuffled native antigen orfragments thereof.

In yet another set of experiments, tumor inhibition assays will becarried out. Two weeks after the last immunization, mice will bechallenged using tumor cells expressing the corresponding vaccineantigen, and protection against tumor growth will be measured. Theseexperiments will show that the presence of the HCV NS3/4A platformprovides a more robust DNA immunogen, as compared to immunogens thatlack the NS3/4A platform, and that the presence of one or more NS3/4Aprotease cleavage sites within the antigen also improves immunogenicity.The assay will also show that the presence of shuffled HBcAg antigenicfragments (e.g., SEQ ID NOs: 1191-1198) within the antigen will providea greater immune response than the unshuffled native antigen orfragments thereof.

In still another set of experiments, quantification of HBcAg CTLresponses will be measured by flow cytometry (Tetramers and Dimer-X).These experiments will show that the presence of the HCV NS3/4A platformprovides a more robust DNA immunogen, as compared to immunogens thatlack the NS3/4A platform, and that the presence of one or more NS3/4Aprotease cleavage sites within the antigen also improves immunogenicity.The assay will also show that the presence of shuffled HBcAg antigenicfragments (e.g., SEQ ID NOs: 1191-1198) within the antigen will providea greater immune response than the unshuffled native antigen orfragments thereof.

Example 22

A similar methodology as that provided in EXAMPLE 21 can be applied toevaluate any DNA immunogen provided herein. More specifically, it iscontemplated that DNA immunogens that are codon-optimized for expressionin humans and which encode the HCV NS3/4A platform and one or morefragments of the antigens provided in SEQ ID NOs: 1016-1034, SEQ ID NOs:1146-1173 and SEQ ID NOs: 1210-1328, wherein said fragments areseparated by NS3 protease cleavage sites will effectively primeantigen-specific CTLs, stimulate antigen-specific proliferative T cellresponses, and induce production of antigen-specific antibodies inanimals when these DNA immunogens are delivered by various DNAvaccination methodologies. Examples of antigen fragments of SEQ ID NOs:1019-1021, SEQ ID NO: 1146, SEQ ID NOs: 1150-1166, SEQ ID NO: 1168, SEQID NO: 1170, and SEQ ID NO: 1172 separated by the NS3 protease cleavagesite NS3/4A are presented in SEQ ID NOs: 1122-1145. Although thefragments in SEQ ID NOs: 1122-1145 are separated by the NS3/4A proteasecleavage site, any NS3 protease cleavage site can be used (e.g., NS4A/B,NS4B/5A, and NS5A/B). Additionally, it is contemplated that DNAimmunogens that are codon-optimized for expression in humans and whichencode the HCV NS3/4A platform and a plurality of antigenic fragmentsfrom the antigens presented in SEQ ID NOs: 1016-1034, SEQ ID NOs:1146-1173 and SEQ ID NOs: 1210-1328, separated by NS3 protease cleavagesites, including antigenic sequences in various orientations as seenwith the HBcAg from earlier examples, will also effectively primeantigen-specific CTLs, stimulate antigen-specific proliferative T cellresponses, and induce production of antigen-specific antibodies inanimals when these DNA immunogens are delivered by various DNAvaccination methodologies. In some embodiments, it is contemplated thatthe DNA immunogens, which are codon-optimized for expression in humansand which encode the HCV NS3/4A platform and one or more fragments ofthe antigens provided in SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173and SEQ ID NOs: 1210-1328 separated by a NS3 protease cleavage site willbe more effective at priming antigen-specific CTLs, stimulatingantigen-specific proliferative T cell responses, and inducing productionof antigen-specific antibodies in animals than conventional DNAimmunogens that encode the antigens alone.

DNA constructs encoding the HCV NS3/4A platform and fragments of theantigens presented in SEQ ID NOs: 1019-1021, SEQ ID NOs: 1146-1173 andSEQ ID NOs: 1210-1328 separated by NS3 protease cleavage sites,including antigenic sequences in various orientations, are made. SEQ IDNOs: 1098-1121 presents codon optimized fragments of antigens presentedin SEQ ID NOs: 1019-1021, SEQ ID NO: 1146, SEQ ID NOs: 1150-1166, SEQ IDNO: 1168, SEQ ID NO: 1170, and SEQ ID NO: 1172, wherein the fragmentsare separated by NS3/4A protease cleavage sites. Although the fragmentsare separated by NS3/4A protease cleavage sites, any NS3 proteasecleavage site can be used. Additionally, although the fragmentspresented in SEQ ID NOs: 1098-1121 are configured in a naturallyoccurring order, separated by NS3 protease cleavage sites, fragments invarious orientations, similar to the shuffled fragments of HBcAg in SEQID NOs: 1191-1198, are made. The shuffled fragments of the antigenspresented in SEQ ID NOs: 1019-1021, SEQ ID NO: 1146, SEQ ID NOs:1150-1166, SEQ ID NO: 1168, SEQ ID NO: 1170, and SEQ ID NO: 1172 arealso separated by an NS3 protease cleavage site. Codon-optimized DNAconstructs encoding only the fragments of antigen presented in SEQ IDNOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ ID NOs: 1210-1328 orencoding the NS3/4A platform and the fragments of antigen presented inSEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ ID NOs: 1210-1328without NS3 protease cleavage sites are also made for comparison. Codonoptimized DNA encoding the HCV NS3/4A platform and fragments of antigenpresented in SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ IDNOs: 1210-1328 in various orientations separated by NS3 proteasecleavage sites are cloned into the pVAX1 expression vector (Invitrogen,Carlsbad, Calif.) or other suitable DNA vaccination vectors. Once theconstructs are made, they are provided to animals by a DNA vaccinationmethodology (e.g., injection, electroporation, such as MedPulser®, orintranasal or transdermal delivery). Analysis of the presence and amountof antigen-specific CTLs can then be made before during and afterseveral introductions of the constructs (e.g., an initial introductionfollowed by one, two, three, four, or five boosting events). It will beshown that the presence of the HCV NS3/4A platform provides a morerobust DNA immunogen, as compared to immunogens that lack the NS3/4Aplatform, and that the presence of one or more NS3/4A protease cleavagesites within the antigen also improves immunogenicity. It is alsoexpected that the presence of shuffled antigenic fragments within theantigen will provide a greater immune response than the unshufflednative antigen or fragments thereof.

The following describes these experiments in greater detail.

Plasmids containing the codon-optimized (human) DNA immunogens encodingthe HCV NS3/4A platform and fragments of antigen presented in SEQ IDNOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ ID NOs: 1210-1328separated by the NS3/4A protease cleavage site will be grown in BL21 E.coli cells, and sequenced for accuracy. Although the fragments ofantigen presented in SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 andSEQ ID NOs: 1210-1328 are separated by the NS3/4A protease cleavagesite, any NS3 protease cleavage site can be used (e.g., NS4A/B, NS4B/5A,and NS5A/B). The NS3/4A platform is separated from the fragments ofantigen presented in SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 andSEQ ID NOs: 1210-1328 by an NS4A/B cleavage site, although any NS3protease cleavage site can be used. In the construct, the NS3 platformis separated from the NS4A by the NS3/4A protease cleavage site,although any NS3 protease cleavage site can be used. Plasmids containingcodon-optimized nucleic acids encoding conventional fragments of antigenpresented in SEQ ID NOs: 1016-1034, SEQ ID NOs: 1146-1173 and SEQ IDNOs: 1210-1328 will also be grown for comparison. Plasmid DNA used forin vivo vaccination is then purified using Qiagen DNA purificationcolumns, according to the manufacturer's instructions (Qiagen GmbH,Hilden, FRG). The concentration of the resulting plasmid DNA isdetermined spectrophotometrically (Dynaquant, Pharmacia Biotech,Uppsala, Sweden) and the purified DNA is dissolved in sterile phosphatebuffered saline (PBS) at a concentration of approximately 1 mg/ml.

Groups of eight to ten C57/BL6 mice or New Zealand rabbits are primedwith an antigen-containing construct intranasally, transdermally, intramuscularly (i.m.), or using an electroporation device (e.g.,MedPulser®).

If a transdermal or intranasal delivery is evaluated, an amount ofplasmid DNA that is sufficient to deliver approximately 70 μg-100 μg ofplasmid DNA per dose is formulated with the delivery vehicle. Animalsare then provided the plasmid DNA one, two, three, four, or five timesat monthly intervals. Prior to transdermal immunization, the deliveryarea is shaved.

If intramuscular injection is evaluated, animals are immunized i.m withapproximately 70-100 μg plasmid DNA at the tibialis anterior (TA)muscle. 5 days prior to DNA immunization, animals may also be injectedintramuscularly with 50 μl per TA muscle of 0.01 mM cardiotoxin(Latoxan) in 0/9% sterile saline.

When electroporation is evaluated, animals are immunized i.m withapproximately 70-100 μg plasmid DNA at the tibialis anterior (TA) muscleand immediately after injection, the Medpulser® is applied with a 0.5 cmneedle array set to deliver two 60 ms pulses of 246 V/cm to theinjection site. In mice, one two needle electrode tip is used and whenrabbits are used, one four needle electrode tip is used per injectionper animal. The procedure can be repeated up to three times in mice andup to five times in rabbits at monthly intervals.

If gene gun delivery is performed, plasmid DNA is linked to goldparticles according to protocols supplied by the manufacturer (Bio-RadLaboratories, Hercules, Calif.). Prior to immunization, the injectionarea is shaved and the immunization is performed according to themanufacturer's protocol. Each injection dose by gene gun contains 4-100μg of plasmid DNA. Immunizations are performed on weeks 0 and 4.

The presence of CTLs specific for antigen is then assayed using astandard ⁵¹Cr-release assay. Briefly, spleen cells are harvested fromimmunized animals 14 days after the initial immunization or a boosterimmunization. Chromium release assays are performed as described inLazdina, et al. (2003) J. Gen. Virol. 84:1-8, herein expresslyincorporated by reference in its entirety. Single cell suspensions areprepared. 25×10⁶ splenocytes are restimulated with 25×10⁶ syngenicirradiated (20 Gy) splenocytes pulsed with 0.05 μM peptide, aspreviously described. Sandberg et al. (2000) J. Immunol. 165:25-33,herein expressly incorporated by reference in its entirety.Restimulation cultures are set in 12 ml complete RPMI medium (Gibco).After 5 days, effector cells are harvested and washed twice. RMA-Starget cells (Karre et al. (1986) Nature 319:675-678) are pulsed with 50μM peptide for 90 min at 5% CO₂ and 37° C. Serial dilutions of effectorcells are incubated with 5×10³ chromium-labeled peptide pulsed RMA-Starget cells in a final volume of 200 μl per well in 96-well plates.After a 4 hour incubation at 5% CO₂ and 37° C., 100 μl of supernatant iscollected and the radioactivity is determined using a γ counter. Thepercentage of specific release is calculated according to the formula:(Experimental release−spontaneous release/total release−spontaneousrelease)×100. The results of the ⁵¹Cr-release assay will show that thepresence of the HCV NS3/4A platform provides a more robust DNAimmunogen, as compared to immunogens that lack the NS3/4A platform, andthat the presence of one or more NS3/4A protease cleavage sites withinthe antigen also improves immunogenicity. The assay will further showthat the presence of shuffled antigenic fragments within the antigenwill provide a greater immune response than the unshuffled nativeantigen or fragments thereof.

In another set of experiments, the presence of γ-IFN-secreting CTLs andT helper (Th) cells to antigens in splenocyte or lymph node cultureswill be evaluated using a commercially available ELISpot assay. (SeeCurrent Protocols in Immunology, Edited by: John E. Coligan, Ada M.Kruisbeek, David H. Margulies, Ethan M. Shevach, Warren Strober (2001John Wiley & Sons, NY, N.Y.), herein expressly incorporated by referencein its entirety). By this approach, the number of γ-IFN-secreting CTLsor spots is determined at various concentrations of peptide. Theseexperiments will show that the presence of the HCV NS3/4A platformprovides a more robust DNA immunogen, as compared to immunogens thatlack the NS3/4A platform, and that the presence of one or more NS3/4Aprotease cleavage sites within the antigen also improves immunogenicity.The assay will further show that the presence of shuffled antigenicfragments within the antigen will provide a greater immune response thanthe unshuffled native antigen or fragments thereof.

In still another set of experiments, the proliferative responses toantigen in whole blood obtained from immunized animals is determined. Anamount of whole blood is obtained from the animal (e.g., approximately 4ml from a rabbit), prior to the first vaccination and two weeks aftereach vaccination. The blood is collected in Heparin tubes and the plasmaand peripheral mononuclear cells (PBMCs) are isolated by gradientcentrifugation. The plasma is stored at −80 degrees Centrigrade untilanalysis for antigen-specific antibodies. The presence and amount ofantibodies specific for antigen in the various samples can be measuredusing an ELISA assay. The PBMCs are immediately assayed for in vitroproliferative recall responses using a standard 96 h proliferationassay. (See Lazinda et al., J. Gen. Virol. 82:1299-1308 (2001), hereinexpressly incorporated by reference in its entirety.) In brief,microtiter plates are seeded with approximately 200,000 cells/well andthe cells are incubated with media alone, phytohemagglutinin (PHA) orrecombinant antigen. After 72 hours, radioactive thymidine is added and16-24 hours later the cells are harvested, The proliferation isdetermined as radioactivity of the cells as the counts per minute (cpm)of cells incubated with the antigen divided by the CPM of the cellsincubated with the media alone (sample to negative ration; S/N). Groupsare compared by the mean S/N ratios at several time points). Theseexperiments assay will show that the presence of the HCV NS3/4A platformprovides a more robust DNA immunogen, as compared to immunogens thatlack the NS3/4A platform, and that the presence of one or more NS3/4Aprotease cleavage sites within the antigen also improves immunogenicity.The assay will further show that the presence of shuffled antigenicfragments within the antigen will provide a greater immune response thanthe unshuffled native antigen or fragments thereof.

In yet another set of experiments, tumor inhibition assays will becarried out. Two weeks after the last immunization, mice will bechallenged using tumor cells expressing the corresponding vaccineantigen, and protection against tumor growth will be measured. Theseexperiments will show that the presence of the HCV NS3/4A platformprovides a more robust DNA immunogen, as compared to immunogens thatlack the NS3/4A platform, and that the presence of one or more NS3/4Aprotease cleavage sites within the antigen also improves immunogenicity.The assay will further show that the presence of shuffled antigenicfragments within the antigen will provide a greater immune response thanthe unshuffled native antigen or fragments thereof.

In still another set of experiments, quantification of antigen CTLresponses will be measured by flow cytometry (Tetramer and Dimer-X).These experiments assay will show that the presence of the HCV NS3/4Aplatform provides a more robust DNA immunogen, as compared to immunogensthat lack the NS3/4A platform, and that the presence of one or moreNS3/4A protease cleavage sites within the antigen also improvesimmunogenicity. The assay will further show that the presence ofshuffled antigenic fragments within the antigen will provide a greaterimmune response than the unshuffled native antigen or fragments thereof.

Although the invention has been described with reference to embodimentsand examples, it should be understood that various modification can bemade without departing from the spirit of the invention. Accordingly,the invention is limited only by the following claims. All of thepatents, patent applications, and references cited herein are expresslyincorporated by reference in their entireties.

Example 23

Groups of C57/BL6 mice were immunized twice with 50 μg of either plasmidcontaining a codon optimized NS3/4A gene, a NS3/4A-Betv1 fusion genecontaining a protease cleavage site between NS3 and NS4A as well as aprotease cleavage site between the NS4A and the birch antigen (SEQ IDNO: 1380), or a NS3/4A-Betv1 fusion gene containing a protease cleavagesite between NS3 and NS4A, a protease cleavage site between the NS4A andthe birch antigen as well as two additional protease cleavage siteswithin the birch antigen (SEQ ID NO: 1381) using an electroporationdevice. Another group of mice were immunized twice with recombinantBetv1 protein (rBetv1) in Freunds incomplete adjuvant. The twoimmunizations were 4 weeks apart. The mice were sacrificed two weeksafter the second immunizations and the lymph nodes and spleens of eachgroup were collected and analyzed.

The presence of γ-IFN-secreting CTLs and T helper (Th) cells to antigensin splenocyte or lymph node cultures were evaluated using a commerciallyavailable ELISpot assay. (See Current Protocols in Immunology, Editedby: John E. Coligan, Ada M. Kruisbeek, David H. Margulies, Ethan M.Shevach, Warren Strober (2001 John Wiley & Sons, NY, N.Y.), hereinexpressly incorporated by reference in its entirety). The spleen andlymph nodes from each group were pooled and immediately tested for thepresence of NS3 and birch specific T cells. The ability of NS3-specificand birch-specific Th and CTLs to produce γ-IFN recalled by aconcanavalin-A (con-A) as a positive control, media alone as a negativecontrol, native HBcAg, recombinant HBcAg (rHBcAg), variousconcentrations of NS3/4A CTL peptide, various concentrations of rNS3,and various concentrations of rBetv1 was analyzed via the ELISpot. Theresults of the ELISpot assay are shown in FIG. 22.

The NS3/4A-Betv1 (major Birch allergen) fusion genes showed that theNS3/4A clearly functions as an adjuvant for IFN-γ production. TheNS3/4A-Betv1 fusion genes showed that the liberated NS3/4A-Betv1 fusiongene (SEQ ID NO: 1380) and fragmented NS3/4A-Betv1 fusion gene (SEQ IDNO: 1381) effective prime IFN-γ producing Betv1-specific T cells twoweeks after the second injection, where the recombinant Betv1 antigenfails to do. The data suggests the fragmented NS3/4A birch antigenfusion gene (SEQ ID NO: 1381) more effectively primes IFN-γ producingT-cells than the non-fragmented NS3/4A birch antigen fusion gene (SEQ IDNO: 1380).

Example 24

Groups of C57/BL6 mice were immunized twice with 50 μg of either plasmidcontaining a codon optimized NS3/4A gene, a NS3/4A-Betv1 fusion genecontaining a protease cleavage site between NS3 and NS4A as well as aprotease cleavage site between the NS4A and the birch antigen (SEQ IDNO: 1380), or a NS3/4A-Betv1 fusion gene containing a protease cleavagesite between NS3 and NS4A, a protease cleavage site between the NS4A andthe birch antigen as well as two additional protease cleavage siteswithin the birch antigen (SEQ ID NO: 1381) using an electroporationdevice. Another group of mice were immunized twice with recombinantBetv1 protein (rBetv1) in Freunds incomplete adjuvant. The twoimmunizations were 4 weeks apart. The mice were bled two weeks after thesecond immunizations.

Dilutions of the sera were tested on ELISA plates coated withrecombinant birch protein. A secondary antibody specific for IgEantibodies was used to detect bound antibody. The results are shown inFIG. 23. The results show that when looking at the priming of IgE toBetv1, the DNA constructs do not prime IgE antibodies whereas the rBetv1shows birch-specific IgE antibodies. The DNA constructs are thus notallergenic in that they prime a Th1 type response.

Example 25

Groups of C57/BL6 mice were immunized twice with 50 μg using anelectroporation device with either plasmid containing:

-   -   a plasmid encoding a codon optimized NS3/4A gene,    -   a naked pVAX-1 plasmid    -   a plasmid containing a gene encoding HBcAg    -   a plasmid containing an NS3/4A-HBcAg fusion gene as follows:        -   C1 (SEQ ID NO: 1382) having an active protease but no            protease cleavage site anywhere on the fusion gene        -   C2 (SEQ ID NO: 1383) having an inactive protease and no            protease cleavage site anywhere on the fusion gene        -   C3 (SEQ ID NO: 1384) having an active protease and a            protease cleavage site between NS3 and NS4A but no protease            cleavage site anywhere else on the fusion gene        -   C4 (SEQ ID NO: 1385) having an active protease and a            protease cleavage site between NS3 and NS4A and a protease            cleavage site between NS4A and HBcAg        -   C5 (SEQ ID NO: 1386) having an active protease and a            protease cleavage site between NS3 and NS4A a protease            cleavage site between NS4A and HBcAg and 3 protease cleavage            sites within the HBcAg which is in a naturally occurring            order        -   C5 (SEQ ID NO: 1386) having an active protease and a            protease cleavage site between NS3 and NS4A a protease            cleavage site between NS4A and HBcAg and 3 protease cleavage            sites within the HBcAg which is in a naturally occurring            order        -   C6 (SEQ ID NO: 1387) having an active protease and a            protease cleavage site between NS3 and NS4A a protease            cleavage site between NS4A and HBcAg and 3 protease cleavage            sites within the HBcAg which is in a non-naturally occurring            order

The two immunizations were 4 weeks apart. The mice were sacrificed twoweeks after the second immunizations and the lymph nodes and spleen fromeach mouse was collected.

The presence of CTLs specific for antigen was then assayed using astandard ⁵¹Cr-release assay. Briefly, the collected cells were harvestedfrom immunized animals 14 days after the booster immunization. Chromiumrelease assays were performed as described in Lazdina, et al. (2003) J.Gen. Virol. 84:1-8, herein expressly incorporated by reference in itsentirety. Single cell suspensions are prepared. 25×10⁶ splenocytes wererestimulated with 25×10⁶ syngenic irradiated (20 Gy) splenocytes pulsedwith 0.05 μM peptide, as previously described. Sandberg et al. (2000) J.Immunol. 165:25-33, herein expressly incorporated by reference in itsentirety. Restimulation cultures were set in 12 ml complete RPMI medium(Gibco). After 5 days, effector cells were harvested and washed twice.RMA-S target cells (Karre et al. (1986) Nature 319:675-678) were pulsedwith 50 μM peptide for 90 min at 5% CO₂ and 37° C. Serial dilutions ofeffector cells were incubated with 5×10³ chromium-labeled peptide pulsedRMA-S target cells in a final volume of 200 μl per well in 96-wellplates. After a 4 hour incubation at 5% CO₂ and 37° C., 100 μl ofsupernatant was collected and the radioactivity was determined using a γcounter. The percentage of specific release was calculated according tothe formula: (Experimental release−spontaneous release/totalrelease−spontaneous release)×100. The results of the ⁵¹Cr-release assayis presented in FIG. 24. NS3/4A clearly functions as an effectiveadjuvant for lytic CTL priming. The peak CTL levels for thenon-fragmented HBcAg were higher compared to all other constructs.

1. An immunogenic composition comprising a nucleic acid molecule thatcomprises a nucleotide sequence encoding a heterologous chimerichepatitis viral antigen comprising hepatitis C virus (HCV) NS3/4Aantigen fused to a hepatitis B virus (HBV) core antigen in the absenceof an additional HCV or HBV antigen, wherein the nucleotide sequence ismodified to encode an amino acid sequence that comprises one or moreprotease cleavage site insertions at one or more non-naturally occurringpositions and said immunogenic composition induces an effectivecytotoxic T cell (CTL) immune response specific for one or more epitopesof said heterologous viral antigen.
 2. The immunogenic composition ofclaim 1, wherein said nucleotide sequence is modified to encode a mutantHCV NS3/4A antigen lacking a proteolytic cleavage site.
 3. Theimmunogenic composition of claim 1, wherein said nucleotide sequence ismodified to encode a HCV NS3/4A antigen comprising a mutantnon-functional NS3 protease.
 4. The immunogenic composition of claim 1,wherein said nucleotide sequence is modified to encode a HCV NS3/4Aantigen comprising a mutant NS3 protease with enhanced proteaseactivity.
 5. The immunogenic composition of claim 1, wherein said one ormore non-naturally occurring positions are located between NS3/4A andsaid HBV core antigen.
 6. The immunogenic composition of claim 1,wherein said one or more non-naturally occurring positions are locatedwithin said HBV core antigen.
 7. An immunogenic composition comprising anucleic acid molecule that comprises a nucleotide sequence encoding aheterologous chimeric hepatitis viral antigen comprising hepatitis Cvirus (HCV) NS3/4A antigen fused to a plurality of antigenic fragmentsof hepatitis B virus (HBV) core antigen assembled in a non-naturallyoccurring order in the absence of an additional HCV or HBV antigen,wherein the nucleotide sequence is modified to encode an amino acidsequence that comprises one or more protease cleavage site insertions atone or more non-naturally occurring positions and said immunogeniccomposition induces an effective cytotoxic T cell (CTL) immune responsespecific for one or more epitopes of said heterologous viral antigen. 8.The immunogenic composition of claim 7, wherein said nucleotide sequenceis modified to encode a mutant HCV NS3/4A antigen lacking a proteolyticcleavage site.
 9. The immunogenic composition of claim 7, wherein saidnucleotide sequence is modified to encode a HCV NS3/4A antigencomprising a mutant non-functional NS3 protease.
 10. The immunogeniccomposition of claim 7, wherein said nucleotide sequence is modified toencode a HCV NS3/4A antigen comprising a mutant NS3 protease withenhanced protease activity.
 11. The immunogenic composition of claim 7,wherein said one or more non-naturally occurring positions are locatedbetween NS3/4A and said plurality of antigenic fragments of HBV coreantigen.
 12. The immunogenic composition of claim 7, wherein said one ormore non-naturally occurring positions are located within said pluralityof antigenic fragments of HBV core antigen.
 13. An immunogeniccomposition comprising: a DNA plasmid suitable for mammalian expression,wherein said plasmid comprises a promoter, which is functional inmammalian cells, operably linked to a nucleic acid sequence that encodesa heterologous chimeric hepatitis viral antigen comprising an (HCV)NS3/4A antigen fused to a hepatitis B virus (HBV) core antigen in theabsence of an additional HCV or HBV antigen, wherein said nucleotidesequence is modified to encode an amino acid sequence that comprises oneor more protease cleavage site insertions at one or more non-naturallyoccurring positions and wherein said DNA plasmid induces an effectivecytotoxic T cell (CTL) immune response specific for one or more epitopesof said heterologous viral antigen.
 14. The immunogenic composition ofclaim 13, wherein said nucleotide sequence is modified to encode amutant HCV NS3/4A antigen lacking a proteolytic cleavage site.
 15. Theimmunogenic composition of claim 13, wherein said nucleotide sequence ismodified to encode a HCV NS3/4A antigen comprising a mutantnon-functional NS3 protease.
 16. The immunogenic composition of claim13, wherein said nucleotide sequence is modified to encode a HCV NS3/4Aantigen comprising a mutant NS3 protease with enhanced proteaseactivity.
 17. The immunogenic composition of claim 13, wherein said oneor more non-naturally occurring positions are located between NS3/4A andsaid HBV core antigen.
 18. The immunogenic composition of claim 13,wherein said one or more non-naturally occurring positions are locatedwithin said HBV core antigen.